allison md 3060

AllisonMan..I need does the md3060 marry up with the starting of my 1992 cummings 5.9 300hp ?? My problem started with slow starting ie turn key on,back and forth to start ,4 or 5 times. Troubleshooting the system (spartan chassis wires I found out that there was no 12 volt to the start relay ..(from the start key) the allison box, ran new 12 volt line to relay .. guess what! starts like it question is, what have I by-passed on the six relay two fuse allison black box? I can still change gears, The display (push button selector) still shows up or down ect..thinking at one time there was clicking from the black box,then that stoped (all relays are the same number and all checked out ok)