Hey Guideon, just caught up on your thread. It sounds like you have things well under control, great job!
Were you able to do all of the exercises in the P90X program when you went through it? I have a friend about 75% of the way through now and he said he has had to substitute exercises here and there because he was unable to do some. I plan on doing the program myself in about a year, when my weight is closer to target and my strength/weight ratio is more in my favor.
I could do the exercises, but no way like Tony Horton or the others in the video are doing them. There are some variations in the exercises to make them easier (not easy, easier

) so I used the variations (still do in some excercises).
When I started I couldn't complete 1 pull-up, could barely do 10 to 15 push-ups.
I had to use the chair in pullups, go to my knees during pushups exercises, but that's OK. Like Tony says: just do your best and forget the rest!
I'm getting better at this, can do about 7 pullups now and pumping out 40 pushups with relative ease.
In the yoga department of the program, I'm not that good. I'm still not very flexible, but that's also because I find yoga to be tedious, so I regularly substituted that with a cardio workout.
I tried a P90X routine at the start of my weight loss journey, but got nowhere near halfway through at that time, and the next morning I didn't want to move, my muscles were so sore then

.
So I took the same route you do, lose the weight and get in shape (conditionally) first and get working on the muscles later.