forget wrapping your head around all these percentages and crap. pick a weight that you know you can get for at least 12 reps for your first week (85%) week. just to put a number on it, let's say you can do 120lb for 12 reps. then work backwards to find your new training max- 120 divided by .85 (aka, 85%) = 141. so "141" or 140 would be your new training max. then week 2 you would use 90% of 140, week 3 is 95% of 140, etc.
AGAIN- i just used 120 to show the math, obviously i dont know what weight you can get 12 reps with, you need to either find that or guess.
there's nothing magic about 12 reps either, just pick a weight you can get at least 12 with, if you end up getting 13, 14, 15, whatever, that's fine. this will ensure you are meeting (and surpassing) your required reps on 5's, 3's, and 1's weeks for a while.
you can try and figure out the percentages and all that (which i dont think is hard by any means) if you want to, but the point is you need to drop the weight to something that is low enough that you can get a good amount of reps in. who cares what percentage that turns out to be of your projected max?
that's just how i do it. ive used 5/3/1 for most of the past 2 years, and after reading the book through the first time, ive never had any of these types of questions. dont complicate it, just do what makes sense. i promise you Jim is not sitting around with a calculator trying to figure out what weights he should be using while he deals with his shoulder, nor was he when he wrote the book.