My 2001 Twin Cam Dyna is basically stock with an Arlen Ness heavy breather and D&D Fat Cat exhaust. I replaced the 170 main jet with a 180 and the pilot with a 48, it starts and idles fine at 1000 rpm it will accelerate up to about 2000 rpm then severely breaks up and wants to stall, it will gradually build speed as long as I don't go over 2K. I've drained the Gas tank, checked the vent lines as well as the supply line, I've checked the float for the correct angle, I put my craftsman multimeter on the wires (on the 20k scale) they mic at 2.69 rear and 5.9 front. same scale the coil mics at 5.6. This is my grocery getter and need it the alternative is a 454 3/4 ton pick up...Help me Mr Wizard...I live at sea level...

 

You sure the exhaust is not restricted, baffle coming apart?

My '04 Dyna had a 190 main & 45 slow when it came off the production line. It ran like total crap & popped/coughed like crazy on decel till I finally worked up to a 195 main & 50 slow, with 2 #4 brass washers under the needle to raise it up. And my bike's totally stock except for DK Customs 587 AC. Even stock exhaust.

What do your plugs look like? Black; white/blistered; light-brownish?

What about the vacuum diaphram in top of the carb? Any chance you pinched it or didn't get it on straight when you closed it up after re-jetting?

 

the plugs are very light brown...I never got into the top so no I didn't pinch the diaphragm...when I was in Texas I put a 195 into it because with the intake and exhaust it about threw me off the back when I jacked the throttle to the stop then backed off 1/8th turn...(The test for lean>>>I read)
it came stock with a 170 which was too lean...very fast but too lean...I put nos plug wires and have a "good" used coil coming...and a jet kit which promised will be the cure...
since moving to Fla in July it has progressively
gotten worse until yesterday when any throttle under a load would die, I went thru all the above this morning and got the results I mentioned...tomorrow I will remove the 180 and holder and go with the 190 again...with the 48 pilot jet see what happens then next week when the coil gets here...we'll see again...if nothing works I'll ride it off a pier and into the gulf...
I bought it salvage 3 years ago...I truly believe it is a lemon...I have replace all wheel bearings, Rear was spun, front caliper froze 2 pistons...kept replacing bearings thinking it was the cheap bearings because of the squeak...turns out it was the brake pins and pistons...

 

Flood bike?

 

Gas filter.

 

Not a flood bike or wreck...irate ex-wife I suspect as the tank was ball peened...I bought it from Euhardys in WI...
gas filter...hmmm I took the petcock off to drain the tank, the filter looked good, I want to say glassy looking, no foreign material in it...
the front coil out looked a bit suspect so I scraped it as best I could and is why I suspect it as the source of my dilemma...as I mentioned it seems to progressively getting worse...

 

If you put a Dyna-jet kit in it, that could be some of the problem. a lot of people take that kit out and go some what stock. My 02 has a 195 main and 45 with the needle set up with the washer trick. The idle mixture is about 2 1/2 turns out. This setup worked fine in and around Daytona and in and around Sturgis.

 

How did it run before you rejetted it? Sure sounds like a faulty diaphragm.

 

1) Emulsion tubes in the carb are gummed up. Disassemble, use a lot of carb cleaner and blow out every orifice in the carb.

2) Vacuum leak.

3) Bad diaphragm.

 

That could be the problem right there.

A friend of mine just had the carbs rebuilt in her Yamaha (2002 IIRC), the shop told her that they were all gummed up due to the ethanol they put in the gas and she was having similar symptoms that the OP is describing.
I don't know what kind of swill gas they sell in FL but that might be the problem.