I've been busier ther past few days than I thought (wife had minor surgery, since she was down for a few days I was busy running kids around etc.) so I haven't had a chance to do any more work on this engine. Also, thanks everyone for responding - I've learned a good bit in the course of getting this engine going but will readily admit that I've still got a lot to learn.

ChampioNman, I'll definitely check over every last detail of the link-n-sync, engine timing, etc. I'd be thrilled to find out that the entire issue is my screw-up on a simple adjustment. Is it possible though for one of those problems to only cause problems after 20 minutes or so of running? I'm not arguing, just hoping to maybe learn something.

Red, are you saying that with your messed up jets that it ran ok for awhile first and then acted up? I'll take a look at that if I don't find anything else.

Todd (how come you only caught 5 fish? ), thanks for the suggestion (I probably should have thought of that but sometimes in the heat of battle I overlook the obvious).

Here's my plan of attack. I've got a small tank I can dunk the lower unit in to get pretty close to actual operating depth. While the engine runs at a fast idle, every few minutes I'll take DVA measurements of the coil primary voltages (orange wires), check spark on each cylinder with my timing light, and also keep an eye on engine timing. While that's going on I plan to also add some heat to the coils one at a time with a hair dryer to see if I can get one to act up. After 20 or so minutes of this I'll shut it down and repeat the ignition system tests from the service manual.

Have I missed anything?