It might be hard to do, but you need to find out if you are losing fuel or spark. My guess would be fuel (and not a flooding issue).
Next time it has sat for awhile, and before you actually start it, turn the key to run and let the fuel pump run until you hear the relay click off after 3 seconds. Then turn the key off and back to run again for 3 seconds. Do this 5 times, then try to start it. If it starts and stays running, then that is a good indication that you are losing pressure in the fuel system for some reason.
BRD has a good idea on checking your wiring splice/bypass too. If you aren't getting full voltage to the fuel pump, then it won't be running at full speed, so it won't build up pressure as quick as normal.