Well, I’m glad to hear you are not trying to push it. Lots of runners have a problem backing off before the injury gets serious. I’m assuming you are talking about what is usually called Achilles Tendonitis, but any tendonitis is a repetitive motion injury that requires a change in workload.
These injuries are usually diagnosed by symptom and physical examination, but there is a mild inflammation form of the problem, and a more severe form that involves actual damage to the Achilles tendon. This is of course what you want to avoid.
If you are a seasoned runner, the latter scenario is more likely than if you are fairly new to the sport, or have taken considerable time off so the muscles/tendons have been deconditioned. Actual damage to the structure of the tendon usually takes some time to bring about.
A couple things I note from your report, is that you are strengthening various muscles, and also stretching them. I feel it is important to note that training itself is generally a strengthening process, and the repetition of these movements under pressure is usually what brings about the symptoms after time. In other words, more of the same thing, even in a slightly different form, may not be helping in your case.
While stretching can be a strategic part of your training regimen when the tissue is healthy, again it may induce the same stresses as training/strengthening, in that it is pulling the same physical structures to produce the same stress, only in reverse slow motion. In other words, stretching may be helpful to healthy tissue, but in many cases can aggravate injured tissue. You want to use some caution here. “Range of motion exercises,” or movement of the foot by its own power through its entire range, can be helpful without makiing the problem worse. Again, pulling something that has been damaged by too much pulling can be counterproductive.
On the other hand, healing is best accomplished under some load. This is called modeling. If scar tissue is present, and inflammation is tearing at the damaged fibers and refilling with new collagen, the matrix that results is more organized when moderate stresses are placed on the healing tissue. This is different from just running through the pain. You want to mildly exercise the healing tissue by taking it through its range of motion under a reduced load. This process is best managed by a professional, but if that is out of reach, you just want to keep the area moving occasionally while it heals, avoiding the original activity and intensity that caused the problem in the first place, and avoiding complete inactivity so it can model properly. Swimming is a great activity. Moderate walking is OK, but don’t overdo it.
The last thing I want to address is what is missing from your regimen. Exercise tones or tightens healthy muscle. Moderate exercise can also relax healthy muscle. Stretching can relax healthy muscle, but it can cause unhealthy tissue to splint in self-defense. Healing is optimized when muscle is in a relaxed state. If you are going to bed with tight muscles, they are not going to heal as quickly
One of the best ways to relax muscles before bed is to combine warmth with gentle massage. You can combat the pressures that lead to tendonitis by taking a warm bath or shower, and working your fingers into the tight calf muscles with some soap and warm water as lubricant, working out any knots you may find in the muscle. Small spasms in the muscle tissue can cause the muscle to stay tight even during sleep, which interferes with the healing process. The stiffness you may feel in the morning results from the rebuilding of damaged tissue overnight.
Add this step to your modified routine, and you will release the relentless 24-hour pressure on the tendons of the rear calf that have led to the problem you have.
Best of luck in your recovery!