Are the 8.8 calipers on the correct side? The bleeder needs to be at the top. Just asking cause that is a common mistake that is made.
The only other thing it could be is the master cylinder, if you are not getting any pedal at all. Did the rod to the pedal come with the new MC? The dual diaphragm booster requires a longer rod, if I remember correctly.
I have an 8.8 disc on my 87, no new MC or booster. Doesn't even have a proportioning valve on it, and it stops fine with 35's.
'87 YJ, 4.2L built and bored, 8" of lift, 8.8 rear, AX15/NP 231J, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...