Sniper 1 running poorly

I am constantly having to re-program my Sniper one to get it to run more than a hundred miles on one program. I sent the Sniper back to Holley to have some issues fixed and re-installed it a year ago last Spring. It ran but roughly and I finally found a header that decided to shed the nuts on all the bolts and come apart. Since it is before the O2 sensor, I was sure I had located the source of all my problems with the car running so rich. After $400 in exhaust work, which included removing the electric cutouts I had previously installed on the car, I was back in business and have driven the car to 3 or 4 shows this year. Each time on the return trip home the engine began to miss and last weekend I barely made it home before the car died. I put in a new (original) tune and and got it running but it is now harder to start. I am about done with this version of Holley's fuel injection system. I don't know what to do to make it run consistently.