bypassing ballast with stock ignition module

ive got a 360 on a starting stand and about a year ago the msd 6al box quit working. so i sent it in they "fixed it" and i got it started again. now im getting it ready to be put in the car but at mid to high rpm its misses and cuts out. what im trying to do is put in a stock 5 prong ignition box in to see if my issues is my "fixed msd box" its a magnetic pickup dist and a msd Ecoil and i bypassed the ballast went right from ignition to + coil to top prong on box and i get no spark. but i do get spark when i flip the switch off on the ignition switch...and i have 12 volts on + coil side and a low voltage leaking through on the - side any thoughts