@Wasabko, Everyone is different, YMMV, etc, etc, but here's my experience:
1. I've always done anything up to a 5RM dead cold. Zero warm up altogether. If I am tapering reps to peak at the end of a cycle, I might ramp up to my working weight with three progressive singles. To me, a set of 5 or even 3 is a work set.
By the way, I'm 51 and a high mileage basketball player, but the only weightlifting injuries I've had were from dumping a squat in my 20s, carelessly picking up a kettlebell to move it (not during a training session), and some elbow tendinitis. So I'm not just being young and stupid (at least not the former).
2. I'm a fan of the original PTTP scheme: 5 x 100%/5 x 90%.
It's very easy psychologically to really focus on nailing that first set and then go downhill from there. The 532 scheme with a constant weight is based more on simplifying calculation and reducing plate changes than any difference in training effect. It does give a higher average weight for the session, but I would not expect any noticeable dfference in results. To me, the 100%/90% scheme feels more "downhill" than having to pull the top weight two more sets (albeit with descending reps). I also find it a big psychological boost when you reach a weight for a back off set that was a top set earlier in the cycle.
For programming, I am very partial to 4 steps forward/3 steps back structured wave cycles. I like the rhythm of light, medium and challenging sessions. You don't spend a long time ramping up with a lot of consecutive very light sessions at the beginning, and you don't get into a death march of consecutive heavy sessions at the end.
I worked up to 425lbs at 5'10"/185lbs BW (and 465 on the trap bar). Earlier on (I recall my first cycle ended with a shaky 235 single), I could use small jumps between sessions and end each cycle with a new max. This meant I was doing a lot of sessions at a relatively high percent of my max and there was not a lot of waviness from session to session, even with a "wave" cycle. As my max got higher, this became a problem. If I started a cycle at relatively easy weights, the cycles ended up very drawn out, with waves that were more like ripples, creating an overall linear pattern of a lot of easy sessions early on, slowly ramping into a death march of hard sessions at the end.
Using bigger jumps between sessions in each wave, and smaller jumps from start of one wave to the next, created a much wavier rhythm of easy, medium and harder sessions within each wave and each cycle.
I also did a lot more back cycling before trying for a new max, rather than feeling I had to end each cycle with a PR.
3. Don't have much to offer here. I'm not a bench presser. The DL starting position problem sounds like a mobility issue. Are your hamstrings tight? Have you tried a sumo stance (I prefer medium/narrow sumo)? Other workarounds are using a trap bar or lifting off blocks to reduce the range of motion.
4. I just pace around between sets. Alternatively, I may alternate my DL and press sets. This way I rest a little less than I normally would between sets, but still get more total time between sets of the same drill (less time between DL and press, but more time between DL and next DL).
Between reps, I don't really think about it. With lighter weights I might do consecutive reps without standing up and resetting. With heavier weights I do stand up and reset, but I don't worry about how much time it takes. I don't deliberately take a long time, but I never want to feel rushed.
5. You can include other lifts. Chin ups or pull ups and ab work are fine after deadlifting. Swings you have to be a little careful about since they overlap so much with deadlifts. Just be conservative, monitor how you respond and make adjustments as necessary. The easy strength/40 day template tends to use a lower and more constant weight, so you can get away with more lifts and more ballistic reps. If you look back through the blog, Pavel has a couple of article about combining swings and DLs, but IIRC none are more than 3 days/week and don't use the PTTP template.
Bear routine should be done less frequently, 3x/week, because of the greater volume and need for recovery. I once did a hybrid routine, with additional back off set but fewer than in the bear, that was 4x/week.
Hope this helps.