2000 Pontiac Grand Prix Shifting/hesitation when fully warm

Have a 2000GTP. Has an Intense 3.4 pulley and updated roller rockers. Ever since I have had the mod done, I have an issue with the car running fine on short trips (less than 1 hr). But when it goes for awhile something goes amiss. Coming off of highway speeds, during city traffic it wants to stall. Dealer told me it was a vacuum leak. Chased it for awhile; replacing the vacuum lines, the tees, the plug wires, the computer. Still did it. Then replaced the MAF, IAC and also the TPS. It seems to go back to normal and then it acts up.
feels like it does not know when to shift from one gear to another. Especially a problem during acceleration from a stop.
Multiple Pontiac dealers have looked at it and even drove it overnight. Problem does not resurface if the trip is short.
I did have the exhaust and catalytic converter replaced a long time ago. Now the stock unit is back on the car. Just not sure if the stock CAT coulb be the issue. How would I know since the diagnostics do not show much else. The slightly smaller pulley should not be the cause of this but now i'm not sure about that either.