How many miles you have on the bike? If you are nearing an interval requiring the replacement of the fuel filter, you might go ahead, and replace the fuel pressure regulator while you are in there (only a few bucks more, and hard to test functionality accurately). If it is sticky, it could cause an intermittent stutter that is a serious pain in the neck to diagnose (pressure measures good most of the time, or whenever someone looks at it). Mine took me 18 months to finally catch. This one will not throw a code unless you have a closed loop engine (O2 sensors).
Sometimes you can have an injector wire that has broken, inside the insulation, that looses connectivity at a particular rpm/load combo (vibration issue). Depending on which wire is broken, you might not throw a code for this one.
A pinhole in an inner fuel line could cause a stutter, but would tend to be pretty much consistent, but would not throw a code on an open loop engine.
A fading map sensor might yield inaccurate results at higher loads (lower vacuum). Faulty TPS sensor could also yield false load indications (already shown to be OK, just including for completeness).
I've read that the crank position sensor, if weak, could cause stutters, without necessarily throwing a code. However, looking at the design, I have a hard time seeing how it could miss crank notch counts without throwing a CKP sync error.
I don't know when HD went to closed loop systems (O2 sensors), so forgive me if your scoot is closed loop. If you have O2 sensors, my gut tells me that if one is fading, it could cause mixture problems resulting in stutters.
Just some ideas. Just know that I do know how you feel. I been there brother.
Be sure to replace both exhaust seals, and all exhaust torca clamps. Verify whatever you have for a support for the 'Y' pipe. I don't know how yours is, but mine can break and not show until disassembled, but definitely cause cracks if broken. Loosen all exhaust connections, then tighten them to proper torque and in the correct sequence. This will minimize stored stress in the exhaust system mounting, and minimize system vibration. Normally, cracks occur from excessive vibration, due to one or more loose connections, even if brief, or the combination of high heat (normal) and stored stress in the system mounting (such as when the system does not line up and you have to muscle a pipe into position before tigntening it).
You want the pipes to line up where they should go before tightening anything, and stay that way as you tighten. WD40. in the connection joints, is your friend here, just to remember to disregard initial smoke as it burns off. It doesn't last long.
Do polish your pipes free of finger prints and such before firing up the scoot after exhaust system work. You don't want any such to burn in to permanent.
Enjoy,
Rich P