I recently purchased an '00 si from an individual and he mentioned due to the MSD ignition, the car runs rough for a few minutes after fueling up. I have recently noticed that also seems to happen when starting after turning off the car while running the air conditioner, but can't say this is always the case. By running rough, I mean the car often takes 5-10 cranks to get it to started and after starting runs at very low RPM (barely staying in a running state) and just chokes/sputters as the RPM gradually increases to a normal idle just under 1000 RPM.
The car has the following relevant fuel system/ignition mods:

MSD SCI ignition
MSD Blaster HVC coil and wires
MSD Dial Rev. Limiter
Venom High Flow Fuel Rail and Injectors
P28 chipped ECU with OBD2 conversion

Any thoughts or clues as to why this might be happening and where I might start to investigate? Thanks!

 

Fuel pump might be losing its prime. Mine takes longer to crank when its REALLY low on gas. I'd check your fuel pressure to start. Either that, or the injectors are too big for the application.

 

Oh yeah, mine's blue too.