If you are using the stock fuel pump relay to provide power to one or more of the pumps, check the wiring between the relay and the coil. That relay can get very hot, especially when the draw is highest under load, and that can lead to an intermittant condition. The interconnection VW designed will shut down the fuel pump if it does not sense power to the coil. BTDT

Another thought, what is triggering the MSD to fire? If it is the Hall sensor in the distributor, that sensor has been known to fail with the symptoms you describe. Again, BTDT

Dave Zaslow