That was a very helpful clarification. The rough answer is that in Wendler's programs, at least in the new 5/3/1 Forever (pp. 15-6), he specifies that the supplemental work generally programmed with the main lift can be done with an alternative. Rack Pulls, Incline Press, standard bench with different grips, front squat, and box squat are all on the lists of options, so you are fine in that regard. Note that Wendler now differentiates supplemental from assistance lifts. See his recent books for details, but basically the supplemental lifts are still big barbell work, while the assistance work tends to be lighter and using bodyweight or dumbbells, particularly accounting for three categories (push, pull, and single leg or core).
Important note: if you are using an alternative lift, you need to calculate its own training max (TM). So, if you are doing 5x5 at 70% for front squats, that should be 70% of the front squat TM, not 70% of your back squat TM.
Regarding the substance of your program, I think it would be better to stick to just one each day (noting that you might change which alternative you use after a few cycles, as by using front squats for 3 cycles, then box squats for 3 cycles). Best would be to pick an exact program you want to do and just change the supplemental work to the alternative lift.
It might look something like this:
Main: Deadlift 5/3/1
Supplemental: Rack deadlift 5x5
Bench press day
Main: Bench press 5/3/1
Supplemental: Narrow grip bench press 5x5
Assistance: Dumbbell rows
Main: Squat 5/3/1
Supplemental: Front squat 5x5
Main: Press 5/3/1
Supplemental: Incline bench press 5x5
Assistance: Pull ups