The order of the main workouts doesn't make much difference - I even remember Jim Wendler saying so himself.
Furthermore the precise choice of the assistance exercises doesn't make a huge difference - the system is all about driving up the four main lifts. Everything else is almost perfunctory to this main objective.
These are - in my opinion - the most important tenets to adhere to:

- Use realistic maximum weights when doing your calculations and then calculate 90% of this number to give you your training max. Your workout percentages are then calculated of this training max. Don't cheat on this step. The workouts will feel easy at first, but with time they will start to get very difficult indeed.
- Don't always push too hard on the final set - just do it when you feel particularly on-form. Always leave a rep or two in the tank in any case.
- Be careful doing deadlifts twice per week (i.e. boring but big sets + main 5/3/1 set). It could well be wise to reduce the weights below 50% of Training Max for the Boring But Big sets. It is very easy to get overtrained on deadlifts.
- Don't push too hard on the assistance exercises. They should feel relatively easy. You're just looking to get in the reps without breaking too much of a sweat doing them.
- Take advantage of the Boring But Big sets to attempt to improve your form on the main lifts. For example - for many people - this means going down lower on squats, or else on deadlift actually resting the bar on the floor before pulling it up again. If you have the opportunity have a proper coach watch you to give you feedback on your form.

Anyway, that's my $0.02 on the subject.

I'll answer all points of your post..
First off - I think that it's generally better to train the main lifts twice per week, hence I put my Boring But Big sets on another day to the 5/3/1 sets. Here's what I do:

Monday
Military press 5/3/1
Bench press Boring But Big
Accessory work (lat pulldown + lying tricep extensions) all on 3 sets of 10-15 reps

Tuesday
Deadlift 5/3/1
Squat Boring But Big
Accessory work (ab raise with dumbell)

Thursday
Bench press 5/3/1
Military press Boring But Big
Accessory work (dumbell rows)

Friday
Squat 5/3/1
Deadlift Boring but Big (albeit with less than 50% of Training Max, and usually 3 sets rather than 5)
Accessory work (Ab machine)

I rest 2 minutes between accessory sets, and occasionally superset the exercises on the Monday workout.
To anwer your second question - I just pick a weight that doesn't tire me out too much and do 3 sets, normally between 10 and 15 reps. Some days when I feel worn out I also skip the accessory exercises. My reasoning is simple - if I'm feeling worn out then I need to be careful to ease up in gym. My focus is on increasing the four main lifts, don't really care so much about the accessory exercises.