Those cushy new shoes are probably overworking the peroneal  (fibularis) muscles that prevent the ankle from rolling outward. These  muscles are also plantarflexors, which might also be overworked at this  point.

Re-reading your post thoroughly including the  goal, the pieces of the puzzle are there. Running 4 years ago means you  still remember how to push yourself. Your goal indicates you are working  toward being in shape - in other words you might not be as rerady as  you need to be to push like before. You may have gained weight which  could overwork the plantarflexor muscles, which at this time are not  what they used to be.

So far your damage control has  involved rest, ice and stretching, which are probably the top 3  recommended ways to deal with running injuries. All of these approaches  are overrated as ways to rehab an injury, and can even do more harm than  good. Let me explain..

Rest is a good way to prevent  runners from doing further damage to their legs, but its benefits often  stop there. If rest was really good for us, we could rest our way to the  next marathon.. why bother training? Rest is a good way to avoid  confronting pain, but not a good way to get the tissue to remodel itself  for the sport you are now avoiding. It may not hurt any more, but it  may not heal better and stronger with no load of any kind placed on the  injured tissue. It's not like gluing the handle back onto a teacup and  waiting for it to set. It's more complicated than that. When you are  dealing with broken bones, there is time allowed for them to knit back  together, but the real strengthening of that bone happens when it is  used. Same with soft tissue like muscle, so don't let anyone talk you  into a theoretical "healing" period that may never come. That's like  what you were on for the last four years.

Another thing  to know about rest is that rest in itself does not cure soft tissue  dysfunction, which is what you may be experiencing right now. I'll give  you an example of what I mean by how I handled my own injury today.  While doing yardwork, I strained the flexors of my forearms when trying  to pull roots out of the ground. These muscles are always on the edge  in my line of work, and extra tired today from hours of use outside.  When the muscles went into a cramp I could feel a painful spasm that  might ordinarily last for days and prevent me from working. I followed  my own advice and began working with them right away, moving them  through their full range to make use of "reciprocal inhibition,"  otherwise known as Sherrington's Law, which states that a muscle in  contraction prevents the opposite (antagonist) muscle from contracting.  We use this to handle a "charly horse" by having the victim straighten  the knee. If your quad were to cramp, you would flex the knee (if both  are cramping at the same time, may God help you).

While  extending these flexors by contracting the opposite muscles, I held the  flexors to feel for the cramp. When I found the active spot, I kept  firm pressure on that spot until the flow of blood to that area was  reduced and it had to relax. Then, I resumed reciprocal motion and  repeated until the cramp was gone, the memory of it gone until your  question reminded me just now. If I had let that thing go limp and  nursed it along the rest of the day, a neuromuscular pattern of feedback  between the sore muscle and my awareness of it could have lasted for  days. There are many, many cases of post accident trauma that keep sore  spots active for a lifetime. The sooner you nip it in the bud, the less  chance it has of perpetuating itself.

When these things  happen, the cause is often simple overuse. You can spend a lot of time  in limbo wondering what you did wrong, all the while making it worse by  not attacking it in a timely manner. Now I will address ice and  stretching. I have, and continue to use both, but they are overused by  many athletes.

Ice is by nature a hostile substance. If  it had healing properties we could all live naked in Alaska and reap  the health benefits. Instead, we find that frozen skin and muscle tends  to hurt - think frostbite - and this is not a good hurt. It's true that  if you leave ice on an injury long enough it will numb the pain, and it  is by no coincidence also true that people who have nearly frozen to  death report a pleasant feeling of warmth and numbness before they were  rescued from certain death. We know it takes pain away, and we so fear  pain that ice is highly prized for its analgesic properties. The only  problem is it does not help tissue to heal, but it can and does do a lot  of damage to those who overuse it. I will hear from those who swear by  its effectiveness and have trophies to show for it, but the fact that  they have survived their self-treatments does not mean they have  benefitted from them.

In cases of acute injury where  severe swelling occurs, ice can prevent the swelling from cutting off  blood flow in neighboring tissue by inducing vasoconstriction. This is a  case of the lesser of two evils, and that's how we are supposed to use  ice. When we habitually use it to kill pain, especially in conjunction  with stretching, we set ourselves up for potential damage to the treated  tissue that is self-inflicted. For those blessed with enough  flexibility that it doesn't matter what they do, more power to them. For  everybody else, listen up: You should never stretch cold muscles, even  in cases where a stretch might otherwise be OK. Back to ice, it is  circulation that heals, and circulation can be enhanced briefly by the  strategic use of ice (which is how I use it), but the general effect  when overused will be to inhibit circulation, and all the immune system  activity that goes with it. The point is to know when to quit. The body  responds to challenge, which is the only reason ice can help. I  challenge my feet by pounding the pavement, but not pounding them with a  sledge hammer.

In your case, you followed cold with  heat, which ordinarily is a good practice - as long as you are not  dealing with an acute injury in which something popped, pulled, or tore.  I'm optimistic that is not so in your case, and I'll tell you why after  I discuss stretching...

Muscles are intrinsically  elastic through the full range of motion of the joints they act upon, at  which time there is an assist from ligaments and other tough tissues to  keep the joints from dislocating, which the muscles could allow by  themselves if they weren't always in a state of partial contraction.  When you think about a muscle as a rope of many bundles of fibers, each  of which is a chain of millions of elastic cells that contract and relax  in unison to cause movement or stasis, it makes you wonder why we think  we could actually "stretch" them at all if they were truly relaxed.  Fact is, that's pretty hard to do, if even possible. What we know we can do is force a muscle to elongate against its own tendency to shorten,  which is otherwise known as an Eccentric Contraction. This is also by no  coincidence the way we injure muscles during exercise. What many  athletes do when they "stretch" is simply a slo-mo version of this kind  of injury. Normally, a busted muscle cell here and there is not too much  an insult to fix along with all the other stuff that goes on during  recovery, but all too often a stretch delivers the final blow to an  already tired and worn band of tissue, and an injury occurs. It's not  like there's always a night-and-day physical difference, but a change in  how the muscle acts and reacts, and whether or not it remains under our  conscious control. A little damage and you may get sore, more and you  may get a cramp or a knot. Still more and you may have a pull or tear,  but most of the time, the damage flies under the radar and a muscle  becomes stiff or "dysfunctional," which is a blanket term for muscle  that is stiff, limp, or a combination of both. Much of the damage we  sustain as runners falls into this last category.

Recalling  my example, I took dysfunctional muscle like a bull by the horns and  rather than simply stretch it, or force it to elongate against its own  tendency to contract, even ball up, I kept the conflict within the  extended family of arm muscles that perform a tug of war on my joints  every day. The "stretch" was simple reciprocal movement, which made use  of the body's built-in method of cooperation by only allowing the  stretch to be accomplished by the opposing muscle as a guarantee there  would be no further damage from eccentric contraction, in keeping with  Sherrington's Law. All stretches should be done this way, or not at all.

Back  to your leg and why it can hurt, where and the way that it does. As you  can imagine, muscle is rich in nerve endings, much of which are  necessary in order for the brain to know when it is OK to contract and  when to back off. All of this elaborate feedback would overwhelm the  most sophisticated supercomputers, so it is no surprise that the brain  does not always know what is going on inside our muscles either. Sure we  feel pain, but it is often coming from some other place than where we  think we feel it. This is because pain actually does not exist except as  a construct of our minds, and it requires interpretation and mapping  into a conscious perception of danger or damage. A famous example of how  this often goes awry is the general feeling of chest and arm pain  before or during a heart attack. The problem is a section of the heart,  but it is "felt" in many other places because we just happen to be wired  that way. So it is with many muscles of the leg, whose damage or  dysfunction is often perceived in areas where there is no muscle at all.  In medicine, the difference is often determined by testing the area  where pain is felt and finding no added sensitivity in that particular  place. There are also tests of the function of suspect muscles to ferret  out the potential source(s) of pain elsewhere. These mystery pains are  actually quite predictable and can be replicated in others. I often work  from charts of these "referred" pains in order to locate dysfunctional  muscle tissue.

Based on these charts, the painful area  you describe along the malleolus is a classic Peroneus Longus/ sometimes  Brevis referral pattern, and the long layoff, possible weight gain,  sudden return to activity, and cushier (less stable) shoes have probably  all added up to dysfunction above the area where you feel it. The  Peroneal (Fibularis) muscles run upwards along the fibula from the  malleolus, and you can find the sensitive bellies of these muscles in  the nooks and crannies around and between the fibula and tibia, about  2-6 inches above the malleolus and below the top (head) of the fibula. Dig in with lubricated fingers, which is  something I do in almost every shower, to compress the painful spots in  these muscles. The pain in damaged peroneals can be severe enough to  feel like broken bone when pressed (and is sometimes misdiagnosed as  such), yet it will not be as sharp and will not be in the bones  underneath, but in the thin muscles that cling to them. Working them  should feel strangely good despite the pain, a bit like a toothache that  gets less severe when you release the pressure. It may take you weeks  to work these into submission, but probably less time than it took to  crank them up.

Meanwhile, there are the shoes. You may  have seen advertisements for the "MBT" (Masai Barefoot Technology) shoes  that are all the rage with older folks. They are deliberately built to  feel like shifting soil underfoot, which gives the wearer a workout for  the leg muscles. What you've got now is somewhere between those MBTs and  a real running shoe. There are some people out there running in bare  feet or Vibram "Five FInger" foot gloves, with virtually no padding at  all, so the soft ride is another thing for runners that is highly  overrated. Your muscles and joints are designed to handle impact. The  shoes should just be to compensate for the hardness of the surfaces we  run on in modern times. Don't let your shoes interfere too much with the  complex relationship between your brain, your muscles, and the ground.

I  know this was a lot to read, but the topic was generic enough - thanks  to the detail you supplied in your post, to warrant a response that  could benefit many others who may read. SInce they may also not want to wade through all of this, I tried to digest as much as possible into the first few sentences.