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So I rebuilt my KDX motor top and bottom for my hybrid, and so far its been great. BUT for some reason its started cutting out and progressively got worse. I originally thought it to be jetting or a main seal but I think its ignition related. Mods are 36mm PWK, RAD valve, cr250 intake/airbox, and cr250 PC platinum pipe and fmf turbine core 2. Was running cr250 secondary coil, but its now using the KDX200 coil, and it helped sort of, but again its still there. Stator is in the stock setting, double checked that.

It will start and idle first kick but the moment RPMs kick up it goes to ****. Kill switch?

Any help at this point is welcome, really just want to ride

Voltage in the ignition system goes up as revs go up so if there is a voltage related problem in the CDI you could have those symptoms.

Did you clean the stator coil plate locations where the screws contact it? That is the ground path between the CDI and plug/coil.
also unscrew and screw back in the spark plug cap. that connection can get rusty. better yet is to replace that wire.