Cthulhu

So far I have decided to replace headers, fuel filter (and relocate it), air filter, belts, cleaning fuel injectors, I'd LIKE to get rid of all the vacuum and emissions crap.

Is there anything I am missing that I should take care of while the engine is out?

Thanks

RAD4Runner

Good that you thought of having injectors cleaned. I should have done that while my engine was being rebuilt. It would have saved me work.
Consider cleaning the intake manifold/throttle body, too?
Clutch if almost gone
Inspect starter solenoid contacts, fan clutch, engine mounts...

Cthulhu

Good idea on the mounts and fan. Tranny is my next replacement so I will do the clutch then. I will add throttle body, I've heard of guys spraying those out with cleaner and watching mud run out. Thanks for mentioning that!