I thought this was a temporary issue last night when I tried the WOT test, but today just cruising in to work on the back streets, it did it again. This time the engine crapped out big time and I had to putt-putt in to work on what felt like one missing cylinder. The exhaust smelled rich, like a carbon rich smell? This all just started when I removed the stock pipes and put the V&H longshots HS with the stock air cleaner.

I will try to get it back home today and tear it down and check the following:

SVS test with the dollar bill like Cougar suggests
Carb ( last time I checked a couple of months ago, it was all clean inside )
Coils
Plugs
intake leaks ( lapped and ported manifold, O-rings in good condition )
exhaust leaks ( hmmm, would this have any effect )

I think that when I jet and open up the air box, this problem should go away.
Maybe I would consider looking into a new set of Dyna Coils and Ignition.

Are there any do-it-yourself ways to check the coils and stock ignition?

I'm not getting any popping on hard decel, would that indicate I am good on the PMS?

Thanks for all your help, hope I don't have to start a post like this again