The arming / trigger wire for the EFI SHOULD work fine going to the original coil power WITH the ballast bypassed as you say. However, "it might be" that some worn/ old ignition switches cause a "pause" between and glitch the system. There has been some speculation about this, but frankly I know of nobody who has actually had problems
One thing you want to be careful of is to keep your ignition trigger (distributor) and other delicate sensor wires, dressed against ground, AKA the block and body, and do NOT run any of those parallel to either high tension plug wires OR high current/ high power wires such as the coil primary. EMF / RFI etc.
Isn't your fuel pump controlled by a relay coming from the Sniper system?