I have a 1998 Bonneville, that we recently had a replacement OEM engine installed. About 30,000 miles ago. It is a V6 engine with Auto transmission and A/C. With the hot weather we have been having, You can shut down the engine, go into a store for 15 minutes and come out and start the car, and it runs rough for about 10 seconds. Does it every time. One time I put it in gear before it cleared out, and it stalled and would not start for about 20 minutes at least. It turned over fine but wouldn't start. I think it was flooded. What I suspect, is this. I think the engine is getting a shot of fuel, like a cold start condition, even with a hot engine. After the engine clears out, it runs like a champ. I don't ever see any black smoke etc If my theory is correct, how do I correct it. If it is probably something else, I would appreciate any help. .

Replacing the Ignition Control Module (ICM) should solve the problem. The ICM controls dwell, or on time, of the ignition coil's primary winding. When not replaced, the vehicle could experience no- or hard start, long crank time, misfire, lack of power, inconsistent transmission shift points, spark plug fouling, catalytic converter failure, poor fuel economy, or CEL illumination. Common problem and easy to replace. If the problem persists, the Engine Coolant Temperature (ECT) Sensor may be the culprit.

Also check to see if you're actually getting fuel at all.
Those cars are notorious for fuel pumps failing. Check fuel pressure at the fuel rail when it doesn't start.