You can run Wendler somewhat successfully on 5 days a week if you're willing to sacrifice your OHP performance a tad. I actually ran the template into a 4 day a week upper lower power hypertrophy split, so in only 2 days of said program before and it was fine, aside from the fact the second lift wasn't quite as strong. If you flip flop you might get away with doing it for a while though.

The two lifts you'll want to pair on the same day are preferably Squats and OHP. They're the least concurrent as far as I'm concerned. The bench press will use up your traps/delts a lot, making it hard to hold a proper squat position. But shoulders might be tight after squats too. Deadlift is taxing enough it should be standing alone IMO.

What I've been doing this past month was the boring but big template (so 5 sets of 10 after the working sets) and somewhat turning it into 3 days full body workouts, and then having OHP as an arms and shoulder day. So my week looked something like:
Bench Press
Rest
Deadlift
Rest
OHP
Squats
Rest

Pairing Squats and OHP would accomplish something similar here, too. I also find that doing the boring but big set of the other lift was a lot less DOMS inducing (if that was the way you wanted to go).

As far as accessory work goes, You wanna make sure you add in some pulling in there. So maybe barbell/pendlay rows with the bench press, and chin-ups or pronated grip pulldowns on deadlift day. In order to make bench day a full body workout you could add in lunges or goblet or even bodyweight squats. And maybe some push-up/DB bench press variations (close grip would be good to hit the triceps too) to your deadlift day. Add some abs in about twice a week. Or one a day. Hit upper & lower abs one day (cable crunches & leg raises), lower back another (hyperextensions, or good mornings, or glute bridges), and don't forget the obliques (Med ball twists, perhaps?). Or maybe just finish the day with a plank.

Biggest piece of advice I have here is to keep it simple. Try to hit as much muscle as you can with a single exercise. You'll wear yourself out really quickly otherwise. Although if your goal is conditioning, stringing a few diff things back to back with little to no rest is also pretty effective.

http://blackironbeast.com/5/3/1/calculator

this is the calculator I typically use. It's got pretty much all variations of the program possible so play around with it. There's actually a bodyweight template in there. And hey, I'm in your boat with the pull-ups. Keep trying, do them assisted, work that back, if you can find some heavy resistance bands, that helps a lot too! You'll get there!

Hope that helps. And don't hesitate if you have any more questions!

I switched to Wendlers in January, and I've been doing a variation of the Triumvirate template. I switch up my assistance work every three rounds, and just make sure to pick a new move that works the same muscle group as his original template.

He recommends 5 sets but since I'm cutting, that's too much for me, so I only do 3 sets of 10-15 reps for the assistance work.

Below is what I'm currently doing, which is a 4 day split.

Day 1 (Monday):
Bench Press
Incline Dumbbell Flyes
Assisted Pullups

Day 2 (Tuesday):
Squat
Bulgarian Split Squat
Back Extensions

Day 3 (Thursday):
OHP
Assisted Dips
Assisted Chins

Day 4 (Friday):
Deadlift
Front Squat
Decline Situp

I will be trying the following soon

Day 1
Squats
DL 5x 10

Day 2
Bench Press
OHP 5 x 10

Day 3
DL
Squats 5 x 10

Day 4
OHP
Bench Press 5 x 10

This way I get to do each lift 2 x per week.