Tokon, which makes me think of Toofer from 30 Rock, has it right. He usually does. I'm not sure if you understand the program. But let's just say it's a "lost in translation" thing and answer your questions.
I hit 5 reps on my last 5/3/1 week (this week) – 10 weeks into the program (first two sets for max reps) - What do you suggest here? I am thinking of lowering the training max to a number that is 10 lbs less than where I began the cycle (start of the 28 weeks – it was 215, so I would start with a TM of 205) or would this be too low? Would you cap these reps? Other suggestion?
In general, as long as you can get 5 reps with 95% week, you should be good to go. The only time this isn't the case is personal experience and you need to lower the TM (or you are injured, working back, etc.)
I hit 6 reps on the military – I am going to continue with the set up until I can only manage 5, then go back 3 as suggested a million times?
Yes. Again, you may have to adjust based on personal experience. The press and bench press suck at progress, especially in the beginning. This is for a lot of reasons but it's miserable. HOWEVER, the best part of this is that if you keep pounding away at the movement AND keep pushing the rows, and chins and dips and all that shit, when your body adapts and gets stronger, YOU are stronger and can ride that wave. Think about it like this - people always want to put all this weight on the bar, as fast as possible. I understand this but when you take it slower, your body has the chance to build up the volume on the little shit. This is stuff like ab work and lower back work - just pounding the shit out of these. And what happens is your body is ready and when shit gets heavier, you are prepared. Because every new lifter adds weight to lifts that their body isn't prepared for - not just the movement aspect but they can't positions, can't support weight, etc. I've seen this so many times, both sides of the coin. The slow road ALWAYS leads to greater gains if you are smart. And that means doing your due diligence with rows, face pulls, curls, dips, chins, back raises, ab wheel, push-ups, leg raises. It means doing your conditioning work and your mobility. It means jumping rope every day or doing jumps.
I did body weight assistance for upper body for 1st 6 weeks increasing the number of reps each week (the main lift was regressing at this point).. Then I switched to close grip bench on military day and bb incline on bench day – I did them for volume (no reps to failure.. tried to feel the muscles working). I read now that this is too much and these lifts should be programed as supplemental work, correct? I assume I should switch back to body weight or dumbbell work for total reps as suggested in the article on your site?
Do this - pick either the bench or press: choose ONE. Make sure each is TM is set properly. For next six weeks the one you picked: do 10x5 with FSL. Superset that with DB rows. Then ab wheel. THAT IS IT. For the other lift, do 5x5 at FSL. Do 50 chins and 100 dips and leg raises after this session. For each of the BBS and FSL sets, make sure they are strong, fast and on point.
On top set for squats – is it OK to pause at the top for a few seconds? For example, this week I hit about 5 reps then need to stop between each rep – hit 11 total. I fall forward a bit on these sets (stop before it gets too sloppy), but make sure I do not on the fsl sets.
Who doesn't pause at the top? Each rep should be independent. Reps aren't there to be done - they are there to be strong and fast. Once again, quality always trumps quantity.
I am motivated to train 4 days, I am thinking maybe switching to 3 days might be better for my life right now. If I do this, would you recommend going 4 days on an every other day basis (so I would have 4 sessions 1 week and 3 the next) or place the military and deadlift on the same day?
Yes, that is fine. If you aren't getting consistent sleep I recommend pounding the main lift as a goal. That needs to be your focus. Do the other shit if you can or have the energy. But recovery is paramount. And when that is compromised, something has to change to account for it. It's not different than diet: if you ate 1000 calories every day, you'd have to change your training, right? You couldn't train the same way as if you had 5000 calories every single day. This is a very common sense thing but too many times, people don't see the big picture and try to smash 1000 pounds of shit in a 10 pound bag. So be smart.
Remember that this generation of lifters is highly influenced by social media and YouTube videos - thinking snapshots and videos represent the "every day" training. The every day training isn't sexy and isn't video worthy. But it's all those days, the grind, doing the unsexy shit, that makes that snapshot so amazing.
Don't fall for the bullshit!