Apparently....and I'm a novice at these 350 twins... because they have two main jets it's nearly impossible to "tune out" the flat spot when running pods. You just move it around. PJ tried hundreds of different combinations and has got it dialed in, or at least that's the word on the streets. I'm not sure exactly what the mod is....it's a bit proprietary. But he only charges $65 to set them up. I ordered some O-rings and rebuilt them myself so, for less than $75 I can get the carbs "right".
I think the longer K&N filters I have are supposedly the ones to use, and exhaust length has a LOT to do with it. He thinks my pods/mufflers combination will work well.
One thing that will help, but is hard to do: if you can enclose the pods and give each one an opening about 2" in area, and then connect the 2 "containers" together, it will go a LONG way toward balancing the vacuum diaphragms. This is the 'key' to getting those carbs working without flat spots. They "talk" to each other thru the OEM-interconnected, low-efficiency paper filters, which was why they would run fine with filters almost totally clogged (my best friend ran his over 30k miles on the original air filters, riding 2-up with his wife the whole time except when commuting to work!). When this "tunnel" is left open, like when the gasket seal fails or the owner mis-assembles the paper air filters (or if you get stung with the EMGO versions, which have the 'tunnel' hole a little bit out of place, requiring you make your own) and this cross-pipe is not closed into the filters, the flat spot appears.
It comes not from the jetting, but from the action of the rubber diaphragms. So, if they are cracked, get new ones or the problem will NEVER go away. We used to temporarily seal the cracks with Fel-Pro's FelCoBond for a (college) semester while the owners saved up for new ones, but that's all this fix would last.
