hi metex and welcome to SF! trust you will enjoy theprogram and see the benefits just like the rest of us.
as for your questions, herewith my 5 cents worth:
my pullups are not up to par with my pushups, and my squats are far ahead of both
Trust me, you are not alone in this department! I think this a "problem" that most of us experience. Having said that though, squats do get a bit more taxing the higher you go up the lvl's. But to answer your question, according to me, there is really no suggestions. Given the size of your leg muscles compared to the others you use in the program, you'll find that squats will always be "easier" than the pull- / push-ups.
2. This is a personal preference and will vary from person to person.
Maybe you can do the "explosive" type on say D1 & D3 (seeing that time is of he essence) and do slow squats on D2, concentrating on form.
3. I never had to use subs, but my understanding of the program is yes, always perform 3 reps to 1 no matter which sub you use.
Elysium has pretty much answered 4 and 5 the way I would have. The only requirement to lvl up is a sub 5 min on D3. As you work the program, you might find that doing say 25 rounds on D1 and a sub 4:30 on D2, your chances of breaking 5 mins on D3 are pretty good, but nothing is guaranteed - you still need to break 5 mins on D3, irrespective of your performances on D1 & 2.