Well, no change in the stuttering... Almost feels a little worse now. Can really power through it now. Stutters even with full throttle, and gets hung up around 5 or 6k. Almost starting to remind me of when the ECU failed. Hope it's not that, since that'll make me think there's a bad wire somewhere frying them. Or maybe just got unlucky twice? Still gotta finish checking the rubbers. Haven't got the intake manifold off yet to check the throttle rubbers. Can't very well see the back side of them. Fronts don't look too bad.
Next only list is the FPR and associated lines I guess.
slow down your check and changing to many things at once.
you ever mentioned how she idles ? steady? fluctuation ? popping ? smoking? white or black smoke present? these are tell tail signs
make a check list and eliminate as you go ! air , fuel , spark.
1. did you do the valve adjustment ? if you have a tight valve that could cause all kinds of problems
2. make sure your fuel flow is clean and steady! new filter and pump and is working right.
3. now if she idles right after valves are check / correctly shimmed.... you can move onto timing and throttle body sync.
you said you did the gas check for leaks and it didnt show leaks. leave that alone for a sec. just work on idle .
once thats right you can chase down the other issue.
1. mass airflow sensor ( could be stuck or a faulty unit) or just needs to be adjusted . there are articles here that walk you thought it .
2.ECU maybe a bad unit or a short ( probably not )
3.throttle position switch could be a culprit .
most important!!! only work on your bike on a full stomach !
one thing at a time . make sure they are good. before you move on