Sputter at 2k rpm

2000 4.3l v6. After replacing my water pump and t-stat the truck sat for over a week before trying to start it. It didn't start right up and I think I flooded it. I changed the plugs with a set that had a few thousand miles on them. The plugs were good and I rechecked the gap. I finally got it started but there was a terrible vibration in the engine and burning smell coming from the exhaust. The vibration and smell finally went away after several minutes of idling and revving. Is it possible that one or more cylinders were not firing then finally started? Now, this morning when I get up to speed relatively slow it sputters around 2k rpm. Starts bucking real bad. If I slam the gas it goes away until i get to 2k rpm again and hold it there. It finally stopped after 10-15 minutes on the highway going 72-75 mph. Any thoughts? Thanks.

Check your coolant level in you rad. You might have a leak that is going into the combustion camber.

Don't think it's a coolant leak. There were no symptoms prior to water pump replacement...can't imagine this would cause a coolant leak into the combustion chamber. Plus there would be white smoke coming out of the tail pipe...there is none. It sputters real violently then completely clears up after about 15 minutes. Then it runs good. It idles fine and it revs fine in neutral with no load. The other strange thing is, it is only the first start of the day. It sat at work for 7 hours and I had no problem after it sat that long. I need to get this fixed so I can dump this piece of shit. Please help. Thanks.

One more thought. I mentioned that I think it may have flooded and one of the cylinders was not firing. Could this have caused a problem with the catalytic converter...and could it be an intermittent problem?

Check the PVC valve.

When I unplug my is runs rough.

You might have a clogged injector and once it heats up works fine.

Do one of those fuel rail cleanings.

What is a fuel rail cleaning? Never heard of it. Also, could flooding cause this?