Everything matters, Tommy.
I lifted for about a year while I was running but decided to abandon it in favor of running, which tends to shift growth from upper to lower body anyway. While some people are out there running with herniated disks, it sure helps to have a healthy spine, and lifting can be risky in that department. Heel striking doesn't help, either.
Physio's advice about disk and joint health is important but I assume your chiro looked into those things, since that is their specialty. X-rays were no doubt part of the work-up, which is standard chiro procedure. If not, you're probably right about "worthless."
You mentioned the 1-month layoff followed by 3&4 milers, which I assume were run at a brisker pace than your longer mileage might have been. Regardless, the extended time off has an impact on muscle tone, which can lead to issues with posture and running form (something your chiro may have lectured you about). Whether or not you were still lifting during this time, but especially if you were, there may have been some subtle changes that were not evident until they were aggravated by the constant jostling of running. Sometimes, muscle damage is slight enough to remain hidden until the muscle is overworked.
By all means, explore the most critical joint and disk related issues thoroughly, then look into active and latent myofascial trigger points in the muscles of your legs, which can radiate pain throughout the areas you describe, including the lower back.
Read more here: http://www.medicinenet.com/muscle_pain/article.htm
Some areas to check: http://triggerpoints.net/userfiles/Soleus.jpg (dark X shows spot associated with lower back pain, in muscle taxed by running)
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