engine murmur (yes, like a heart murmur)

[bwoodall]

I just replaced the ignition control wiring harness and the engine wiring harness, and now something is happening that never happened before. When I first start the engine, whether the engine is hot or cold, the engine runs fine (in park and drive) for about 30 seconds to a couple of minutes, but when I accelerate the engine stalls for a moment and then kicks in again. After this little murmur, the engine runs fine, even for long drives, but when I turn off the engine, the same thing happens when I re-start it. I'm afraid this minor nuisance will become a bigger problem. Does anyone have any idea what is causing it? (Mechanics here in Puerto Rico are stumped.
Billy in Puerto Rico