Having run this template, I can tell you this by far one of my favorites and something everyone should give a go if you are willing to do the work outside the weightroom (eating, sleeping, conditioning, etc.....the recovery work). Like all templates Jim writes, do it as written before screwing with it. I understand the questions concerning the 20 reps squats and the percentages. Do it as written for six weeks, do something a little less extreme for six weeks, and come back to it and then mess with the percentages if you feel you need to. I've done it both ways, exactly as written (45, 55, 55, 50, 65, 70) and then switching it to 45, 50, 55, 60, 65, 70 the second time around because I am OCD with numbers. To be honest, it doesn't matter. 20 rep squats suck the life out of you all the while making your balls grow larger.
Here are some random thoughts:
Eat...when you think you have eaten enough, eat some more. This template is designed to move the scale, so grow. If you think something like this is worth doing, then it is worth doing right.
Conditioning...the AirDyne will be your best friend the day after your 20 rep squats. Do something to get blood flowing to your legs. If you don't have a prowler or an AirDyne, do something similar (read: easy conditioning) that won't take away from what you are trying to accomplish in the weightroom.
Accessories...adjust the volume to suit your abilities and try to work up to the target reps. I suck at chins, so I switched the weighted chins out for fat man rows and did chins (sets of 3) between the Press BBS sets. Dips, I couldn't do 100, so I started with 5x10 and ended up with 10x10 by the end of the program.
Training max....I can't remember, but I think it is suggested to go no higher than 85%, but like mentioned earlier, it needs to be dialed in. I've been doing 5/3/1 for almost three year and have pretty much religiously followed the 5/3 periodization. I ran this for the first time one cycle after the 3 cycles back reset. Remember, the TM is a tool. The second you forget that, you become the tool.
As Jim put in the write-up, this template is doable. It's not easy and will require some focus, dedication, self-discipline, etc....you know, all the crap that makes people awesome.