Thats exaclty what happened to me, thats why i was asking if it was a wot, my problem was only at wot. I posted about this a few times in other threads, the problem drove me nuts for a few days. They sell and in-line stainless filter from merc for this problem. I also used a scan tool and showed no problems......I glad you found it........

I'm interested in the gizmo you purchased to check the engine. Give us some more details like website, model number, and cost. I'd like to have one myself...

The software is called Diacom and I got through Rinda. http://216.230.203.183/marine/marine.htm It was $579 They also have the regular Mercruiser handheld scan tool which is I believe $399

Well, back to the drawing board. I hoped that I had found the problem in the fuel pump having crap in it but I guess that wasn’t it. I was able to go out twice and have no surging problems but this past weekend the surge came back and seemed worse than ever. Thankfully (sort of) I had my scan tool available. I was able to record the ECU parameters as the engine was surging. Basically the engine will drop anywhere from 300-1000rpm until it pops, then stalls. I can re-fire it and rev it in neutral all through out the rpm range and everything is fine mechanically. Below are some screen shots from the ECU recording that show a 700RPM drop but minimal to no change in any of the ECU parameters. The ECU is showing NO fault codes either. I am basically at a total loss here. I’ve talked to 2 different people who believe that there could be an electrical problem such as a bad wiring harness. Has anyone experienced this or have any ideas? Thanks for any help you can offer.

Sorry for the shots being a little small. OSO is resizing them.

I suspect you may have a clog in the fuel system again. What you are describing is consistent with fuel loss, not spark. Whatever it was that you cleaned out of the boost pump is still in the tank and it has likely clogged the pump again. Or it made it through to the next choke point. You may need to do a tank cleaning and thorough inspection of the entire fuel route to find it. Before doing that if you can hook up a fuel pressure gauge, watch the pressure as it occurs-if it drops down you have another clog.

Thanks for the feedback Ted.

De-ja vu, It took me a couple seasons to figure out.
Actually dixie doug figured it out for me. Same thing
bunch of crap clogging the screen. Metal shavings and
bugs. Theres an old thread on this subject. I thought it was just fountain putting a tank off the shelf with junk in it. Great quality control. Every one with a 496 should
remove this pump and clean the screen. Mine was only
at wot, I was racing a 27 on cumberland and it started
missing, And I was winning, really John

Are you reading your scan tool when the surging begins under load? I would look for lean fueling condition which would back up Teds belief which is also my feeling that you are getting a fuel starvation condition under load that when you back off the throttle the computer is trying to overcome with a richer mixture setting and hence the engine begins to surge heavily or "hunt".
I would invest in a fuel pressure guage, connect it to the shraedder valve on the fuel rail and watch fuel pressures at idle and under load. Use the ranges on the good engine to crosscheck pressures on the surging motor. This will pinpont if your fuel system on the surging motor is having a problem.
Good luck, troubleshooting skill is what makes great mechanics!
Raylar

Thanks for the feedback guys.

Raylar, yes the scan tool data logs in real time then I can go back and replay the file. The screens above are actually two back to back frames. The 700rpm drop was instantaneous.

It looks like I'll be taking a look at the fuel system.