My car will start up and run fine as long as it sits for a couple hours. If i drive it up town and shut it off, it will either not start or start and have a rough idle sometimes stalling. If i let it sit for a few hours it will eventually start right back up and be fine. I was told it was a fuel problem and I replaced the fuel pressure regulator and the gas tank because it had some holes in it. that didnt help. I then did a complete tune up on it, that didnt help, I then was told it could be the egr valve, so i replaced that and that didnt help either. all the sensors check out good and im getting a multiple cylinder misfire engine code. Could this be the fuel pump?

sounds to me like it could be the ignition coils, they usuall have three packs, each pack controls two cylinders, if you having a problem with multiple cylinder misfire it can be the coils, try having it checked out or replaced, and you might want to replace the module as well, autozone might be able to test those for free, but you have to remove it to test it, just so you know. that happened to my delta 88, it was some kind of sensor under the module, but i think it was the coils when i replaced them everything seems to work fine.

so long story short, try the coils and module, see what happens

Coil packs and switching/amplifier module are possibilities, and so are injectors or a fuel pressure regulator leaking down. If you have a fuel pressure gauge, monitor standing fuel pressure once the engine shuts off. If it holds pressure for at least 30 minutes, you can probably rule out leak down. If the pressure bleeds off in a matter of a few minutes, there may be an injector of FPR leak flooding the engine on shut down.

To test this theory, try starting while applying about 1/2 throttle to admit extra air when the engine will not otherwise start. If it starts with extra air, that's an indication of flooding.