Honestly I think you need to read a little bit more on his site, because he’s answered all of those questions in his Q&A- and also provided a lot of other valuable info, but I’ll try to help you out.
1.) It depends on how much weight you lift. a guy who squats 900 pounds isn’t just going to do that on his 3rd set. Start with an empty bar, and work up, making big jumps at first and then smaller jumps as you get closer to what you think your workset would be. If you were going to try a 3-rep max at 225, it might look like:
bar x 5
95 x 5
135 x 5
155 x 3
185 x 3
205 x 3
225 x 3
205 x 3 (optional if you feel like you have more left)
At 495 x 3, it might look like this:
135 x 5
225 x 5
275 x 5
315 x 3
365 x 3
405 x 3
455 x 3
495 x 3
2.) The max-effort upper body day is NEVER chest and shoulders. It is ME Bench, meaning, a day designed to build your bench press. So your exercise selection will be one that will help increase your bench press. A slight difference, but an important one. Honestly I would suggest following the layout strictly for at least 2 cycles (lasting 4 weeks), to give yourself a feel for what works and what doesn’t and what you like and what you don’t.
As for biceps/triceps… One thing I can GUARANTEE you is that your triceps are going to blow up using this program. I don’t know how you didn’t see any triceps work because this program is practically based around it! Benching (if done powerlifting-style, as this program assumes), board-presses, floor-presses are all great tricep builders and you should also be doing 2-3 sets of a tricep isolation movement in your upper arm superset on the RE Upper day. As far biceps, you should be doing 4-6 sets of direct bicep work per week, along with a bunch of lat/back work. For a beginner, that will be enough to stimulate growth.
I will say that I loved this program and made some tremendous strides on it. My arms definitly put on a lot of size, more in the triceps than biceps, but I made some good gains on that too. My shoulders got bigger, my back got bigger and stronger and my legs have definitly blown up. I also think that this program is a lot of fun, as it gets you competing against yourself and every workout you are trying to set a new record, whether it is total weight on the ME days or total reps on the RE days. And for a relative beginner, you can really set a new personal record every session, so that makes it an awesome program to be on. Plus, with the popularity of the program, there are a ton of resources out there and a lot of guys that can help you tailor this program to your goals.
So my final advice to you:
Follow the program by the letter for a pair of 4-week (3 work weeks and 1 deload) cycles, then start experimenting with making changes.