So, I've been kind of a lurker here for some time now. My health is very important to me but I went to a middle school and high school with no gym programs, so prior to going out and trying to teach myself, I had near zero knowledge of weightlifting and other fitness practices. As I'm sure many of you know, breaking in to this scene can be kind of intimidating. I already have my own workout routine, but I feel like I'm probably missing something and am trying to find some new things to incorporate. I'm also a little confused as to where I should "start," as in some ways I feel like I'm already somewhat experienced - just not really that knowledgeable. Also, I have a number of chronic health problems that make sticking to normal fitness plans kind of difficult for me.

Well, that's the short version; here's the long one.
I was a very skinny kid up until somewhere around age 8, at which point I started getting chronic colds and weird headaches and pains that would put me down for days at a time. I ballooned up to a not-quite-worrisome level of overweight by the time I was 13 and haven't really been able to shed it entirely since. Health problems notwithstanding, I get ample exercise - more than a lot of my "fit" friends - but I'm the type that bulks up quickly and so while I have learned ways to lose fat, I seem to put it back on pound-for-pound in muscle.
For a long time my doctors told me that my discomfort and weight were both results of lack of exercise (which didn't make sense to me but I believed them at the time.) But, I could never add more than I was already getting (as much as five two-to-four hour workouts a week.) Being 20-50lbs overweight made it hard for me to do more effective cardio exercises like running - I had never learned the proper form and it was much too painful. I tried and was rewarded with a number of sprained ankles and dislocated kneecaps. I would occasionally make some visible progress, only to be taken out of commission by a two-month ear infection or the like, and then get back to my routine in more or less the same shape I started in.
Fast forward about ten years, and I'm diagnosed with a fairly severe sleep disorder (narcolepsy/idiopathic hypersomia/other complicated Latin term depending on the doctor you ask.) Also, apparently carrying around a 45lb backpack of textbooks in high school (no lockers) didn't do me any good, as I have a fairly warped spine. (Working as a stocker at a grocery store at the time probably didn't help matters.) The pain stuff is still more or less unexplained, but I've got my fingers crossed that it'll fade if I get my weight down and start managing my other conditions.
In college I started a more regular, rigorous martial arts regimen, as well as biking to and from school. It didn't cut my weight the way I would've liked, but I've filled out a lot more and I at least don't look so much like a lump. I was feeling pretty good until I broke my leg a few years back and was off my feet for about three months. Normally I think most people in my position would've been doomed by that kind of hangup, but it turned out to be a blessing for me.
After the break I had a totally inexplicable two-year run of more or less perfect health, and to cure my cabin fever from being stuck in my house with a cast (it was dead winter and very wet/snowy) I got a set of freeweights and started doing upper body exercises compulsively whenever I started to feel bored or foggy. Once I was back on my feet I got back to regular bodyweight exercises, started learning about working various muscle groups, and finally overcame my aversion to gyms. I got bounced through a few physical therapy offices, first for my leg and then for my back once my osteopaths noticed how bad my posture was, and three or so years later I'm still doing those routines (I can't believe how long it's taking but I'm definitely seeing progress.)
I still have a few things that hold me back, though. My super-health has faded and I'm now back to my regular strings of colds/infections that sometimes go months at a time; I've learned to work through them but because I have an hourly job to keep up with, they do eat away at my recreational time. I lost my health insurance about a year after my break and so I still have temporary hardware in my leg and ankle; I can feel a tendon slip back and forth over the plate with each stride unless I favor my bad leg. I also lost my prescription coverage for the narcolepsy for a little over a year, and when my sleep went wonky again I totally fell out of my routine for a while. I'm back on it, but it isn't nearly as thorough. My gym changed hours so I can no longer do my stretching/physical therapy before work in the sauna. (Sounds petty I know but that was probably the number one part of my success before - without that start-up in the morning I have a lot of difficulty.) I've also got a number of soft-tissue injuries that I have to be wary of, and work on correcting; loose kneecaps, partially torn rotator cuffs, etc.
I'm pretty sure my situation isn't hopeless, but I do feel like I'm at a bit of a dead-end, or perhaps just not as informed as I need to be. I'm hoping for some help coming up with a new routine, or maybe just some recommended reading for guys in my situation. Like I said above, I'm also kind of muddled about where I should rank myself in terms of experience; knowledge-wise I know I'm a beginner, but in terms of endurance and strength I might be intermediate. (For a fat bastard like myself, my cardio might even be advanced - I get weird looks from nurses when I get my pulse/blood pressure checked.) For those of you that managed to bear with my ramblings, thank you. Any suggestions are welcome.