This sounds suspiciously like a problem I once experienced on a Pontiac. The fuel line ran very close to the head. Once the engine got good and warmed up, it would die off because it was starving for fuel. The cause is called vapor lock. The gas actually boils in the line and turns to vapor that is at higher pressure than the fuel pump can overcome, starving the engine for fuel and killing it off.
To troubleshoot, run the motor until it starts exhibiting the symptoms, then spray some electronic parts cleaner on the fuel line where it runs near the manifold or head. (Electronic parts cleaner comes out of the can colder than all get out.) If the motor responds immediately, you've found the source of your problem.
The solution is to move the fuel line away from the head and/or intake. Usually you can do this by bending the line, but you might want to secure it with some standoffs so it can't move back.
If this ain't it, I ain't got a clue.
