I thought the rule of thumb was never spray below 3000rpm and stop 200rpm before your shift.

Also, it almost sounds as if your FPSS was doing its job. When the rail pressure dropped it shut the system down. Then the static pressure in the rail was enough to activate the system again...this would happen very rapidly and feel like a stutter. Your FPSS may be adjusted incorrectly.

 

Pull your plugs and check them too. Make sure they arent melted. your afr should be in the mid to low 11's while spraying. What jets are you running? If anything like NX 52-31 for 100hp should be right for the 4.8. That puts my 4.8 right at 11.2-11.5 afr at WOT. 57-35 is about right for the 125hp. and 62-41 for 150. I bet the problem was no warmer but check plugs. My msd is set at 3500-5600 so when it shifts gears its not spraying. Saves the tranny. Yeah it sucks out of the hole, but I cant spray off the line until i get a locker.