I can't address your issues specifically, but I'm working on rehab myself--I have myasthenia gravis and went into crisis last summer, spending three months in the hospital. Before I collapsed, I could do curls with a 75-pound barbell and ride 50 miles in a litle over three hours. At my weakest, in October, I couldn't turn over in bed, let alone walk, and struggled to curl a 2-pound dumbbell. I'm still not riding, but I will be in a few weeks, and I'll probably use a cane most of the time, though I can get around without one.
If your insurance will cover professional physical therapy, use it! I can't emphasize enough the value of a pro. I've been an athlete all my adult life and know a fair amount about conditioning, and I learned a lot from them.
Like you, I was once a runner, doing up to 80 miles a week. I switched to cycling in my 40s, about 20 years ago, and it's much easier on the body. I think your plan for the stationary bike is sound if your back will take it (there are recumbents, of course). I've been riding one for three or four weeks, gradually increasing my time and resistance, and I'm making progress. You might even consider a recumbent for your main ride--they're a lot of fun and tend to cause fewer injuries than conventional bikes. I've been looking at them, too, but have to get out from under my med bills first. You also can set up a conventional bike to make it easier on your back.
I'd suggest telling the bike shop guys about your condition to see what they recommend. If the 19-year-old racerboy employee tells you you'll get used to it, go elsewhere. You need to adjust the bike to fit your body, not the other way around.
Above all, don't get discouraged. I'm not kidding--three months ago, I couldn't take a leak without two nurses to help me to the bathroom, and I didn't know if I'd ever walk again. I'm 75 percent back and improving every day.