Definitely OK for the frame and engine not to match, tell em outright, I swappered the motor. either theyre gonna cool, or theyre gonna be dicks and you're fucked - but if they were gonna be dicks you were fucked anyway. That's the shit with cops. they're either gonna fuck you or they aren't. you gotta do the basics like registration and stuff to keep em off yer bak but by the time it comes to being pulled over it's just a roll of the dice and whatever prejudice theyre feeling about you already.
Custom frames you an get a custom frame registered as a custom frame but usually gotta have a shop inspect it, which means it's gotta have all good blinkers and lights etc. kinda like getting a salvage title cleared, similar inspection that says it's road ready. Way easier though is just swapping a vin plate and relying on the fact that probably it's good enough.