I also went through the whole program and the videos a couple of times (it's amazing how much free time you have when you can't walk).
I modified the schedule a little bit so I'm not doing two upper days and then two lower days in a row. Here's what I do:
day1: upper body
day2: lower body
day3: neural charge + light cardio (as I said swimming is great for an injured leg)
day4: upper body
day5: lower body
day6: foundation (lats/biceps)
day7: neural charge + light cardio
That's pretty much my 7 day split. I change things around a bit depending on other activities and just how I feel. You can put foundation/charge days pretty much anywhere in there. The main thing I wanted to do was split up upper/lower days so I'm not doing the same thing two days in a row.
For exercises this is what I do:
Push press (9-15 sets) I do these in 'waves' of 3 sets. So I'll warm up to my max training weight (MTW) then take off 20lbs. Do a set there, add 10 lbs do a set, add 10 lbs (now back at MTW) do a set. I call that one 'wave'. I then do 3-5 waves (depending on which week i'm on at that weight). I usually do 3-5 reps depending on how I feel and what percentage of MTW I'm on.
Incline bench (9-15 sets) same thing.
Flat bench (9-15 sets) same thing here but for the waves I take off 40 lbs and increment back up in jumps of 20. So it's MTW-40, MTW-20, MTW.
For assistance work I usually do one set in between each wave, for a total of 3-5 sets of assistance work per exercise. Some things I do: (all barbell/dumbbell depending on my preference that day). Shrugs, overhead shrugs, rows, rear delt flys (dumbbell only), face pulls (on a machine).
Back squat (9-15 sets) same thing here MTW-40,MTW-20, MTW
Deadlift (9-15 sets) same thing
Foundation (Lats/biceps): the article and videos are pretty clear here. I do that pretty much by the book. I do some pull-ups though. Don't forget your prowler work here.
Neural charge days: These are a bit tricky with a broken leg as a lot of the stuff is jumping. For a while I just did pool work. You can do jumps and stuff in the pool with little impact on your leg. Ask your PT for advice here (they told me I could do vertical jumps and 'sprints' in the pool)
Also, on all training days: I warm up with some form of light cardio for 10 mins, then do some sort of complex with the bar, then do some sort of activation exercise. I got cleared to do cleans on Tuesday, so now I do 10-15 cleans before every workout as my activation exercise. I also swim about 5 days a week (not on lower days-these drain me so much I worry I might drown =D).
By no means is this necessarily the best way to do the HPM program. This is just what I came up with, and it's been working very well for me. Hopefully you can get some idea of what you want to do from this. Also, that was a lot of typing so I may have overlooked something, but hopefully it's pretty clear.