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I've been checking on this thread just to see if you ever came to a solution. My prelude had the same thing happen with 2 ECUs and I never figured it out either. I remember replacing the main relay lessened the problem, but it never was 100%.

That being said, your situation sounds a bit different. If it's only on hot/warm start, it would lead me to believe it's almost certainly something electrical and in the engine bay. Like maybe something is expanding from the heat of the engine (which is no longer being dissipated by you driving and moving cooler air over components) causing a connection not to be correctly made any more after it sits and bakes for a bit.

Checking grounds is the first thing that comes to mind in this situation, and they're also relatively cheap to replace....sadly all I have is that as a jumping off point. Nothing else is really coming to mind.
I would also start checking grounds, wires for cracks, and all connections. Sounds like electrical to me.
Well I took the car down to Dover over the weekend. Started it up and drove for over an hour. Not one problem. Shut the car off for about a hour and it started back up without any problems. Made a few stops along the way back home. Everything worked great. The times I let the car sit varied between 10 min to a hour.

Now On Monday, I drove the car and let it sit for about 20 min. When I started it back up it was spitting and sputtering like it was only running on a couple cylinders. I pulled out onto the road and got on it and it went right away. Briansol, I would try another fuel pump but I just don't have an extra one laying around or the money to go buy one. As for the ground wires, I'm working on getting new wire and re-doing all the grounds. I hope that it works it's self out or that replacing the grounds work. Thanks for the advice.