You're making this far too complicated. First, you don't need to follow percentages at weights like 40%. That's way beyond nit picky. Warm up however, then when you get to significant weight (60-65%), use the percentages.
As far as my understanding goes, you just switch the 5 and 3 weeks. So it's
All based on training max (90% 1RM)
wk 1: 70%x3, 80%x3, 90%x3, work up after this is optional
wk 2: 65%x5, 75%x5, 85%x5
wk 3: 75%x5, 85%x3, 95%x1, work up after this is optional
wk 4: Deload
As far as I know, that's all the setting up you need to do. Maybe you have the option to work up on the 3 and 5/3/1 weeks, but if you're trying to plan out PR's based on percentages of your current all time PR, then you're missing some of the main points of 5/3/1- start too light and push hard when you feel good, don't when you don't.