Okay so.... Back from vacation.
Getting everything back together and to spec. Still have a clutch issue with it not engaging / disengaging making it really hard to shift gears. I have everything set to spec and there is still the missing - not being able to click into gear easy.
The motor runs great though, sounds way better and a bit smoother at lower idle once the motor has got some heat to it. I ran it for a bit then re-torqued the head bolts after noticing a small leak and that seemed to fix it.
Any guesses about the clutch? Im about to quit fiddling with it, seems 1 step forward and two back with it.