In reply to paul walters:
Sorry to hear about your knees and the physio fiasco.
I'm just coming back to running after a few months off, feels so hard, good effort for even trying.
One thing I've always found benefit from are those foam rollers. Doing all the soft tissue on your legs, gluten, etc is a good warm up, but I tend to walk for the first 5 minutes then (really) slowly up the pace. I remember reading somewhere that it takes about 10 minutes for your body to switch into "cardio" mode and about 20 minutes total before you clear the lactic acid. So aim for a 20 minute warm up, alternating between walking and light jogging. If you're worried about your running form add some knee raises/heel kicks.
As for recovery, I usually walk for the last 5-10 minutes and do a quick round of stretching (only about 3/4 stretches) and have some recovery food. Then I do a bigger round of stretching with more exercises before bed, with a bit more of the foam roller. This routine has been working for me so far (touch wood).
The only other thing I can think is less scientific, but my brother came up with it after a long lay off. He created a sort of pyramid training scheme, 4 weeks on, one week off. So for the first 4 weeks, he did one run. Then a week off. Then 2 runs each week for the next four weeks, followed by a week off, then 3 runs, week off, then 2 short and one long run. So it was sort of a 5 month training plan. Don't know if any of this has given you some ideas, it's just things I've tried in the past, best of luck getting your fitness back for kilimanjaro.