Five year old crate engine

So, I have a fairly nice 72 swinger special, 225 on a 3 speed auto. It is all stock and has the original engine. My dad and I took the engine out and bought a crate engine some 5 years ago. Now I'm putting it in and having a few problems.

First of all, do I need to take the oil pan off and clean or lubricate anything? I'm sure the valves need adjusted after they warm up but do they need anything before being run? I figured out how the flexplate bolts to the torque converter but one of the bolts is hitting something and the engine will not turn. Can if spin the engine and tranny backwards or will splitting the engine from the tranny help?

The other project on the engine now is what to do with the manifolds, should I just take them in or can I clean them myself?