Tuning problem or more?

[InsaneWs6TA]

I have a 02 Trans Am pretty heavily modded. Head and cam package, 591/591, 230/230. FAST intake and FAST 90mm throttle body. SLP cold air intake. March underdrive pulley. SLP long tubes with SLP loud mouth cat back. Stage 3 RAM racing clutch with aluminum flywheel. SLP 160 degree thermostat. SLP Mass airflow sensor. All suspension has been modified (Hotchkis) with sway bars and strut tower brace included. Meziere 55 Gallon electric water pump. MSD blaster coils with new wires. SLP 1.8 ratio roller rockers.
Car was computer and dyno tuned after heads, cam, cold air, and throttle body. Made 463 RWHP. Car ran great. About a year along everything but the water pump, coils, and rockers were installed. Car still ran good with small idle fluctuation at cold start. Another 6 months later or so the electric water pump, 1.8 rockers, and coils were installed. Car will run really strong at points, but then start running really rough with hard idle and a lot less power. But 5 minutes later sometimes clears up and starts running good again. This can continue during the whole time car is running. If car is shut off and started back up, will run crappy the whole time. If left over night and started back up in the morning, will run good again.
Just need some help in diagnosing problem. Do I need another computer tune? Seems to be the only solution. Thanks!

[99Redz28convt]

I know this doesn't apply directly, but I had very similar problems with my 90 supercharged mustang. I chased everything an finally fixed it with a new ECM.

[kealap]

Fuel problem maybe? Check fuel pressure when running good and bad. Maybe fuel pump dying.