Five year old crate engine

Heck, you're practically a neighbor! A lot will depend on how the engine was put together. If they used assembly lube everywhere, no other prelube would be needed. If you're installing a new oil filter, I would add a cup or so of oil inside and rotate it around so it soaks in. On a small block, I would fill them but on a slant it makes too much of a mess getting them installed before the oil leaks out. You'll have to figure out what is hitting the flex plate bolts. Pull them all back out and make sure they're all the same. Turn the engine over at least one revolution to make sure it's not something else causing the problem. Hopefully you didn't bend one of the flex plate ears during installation of the engine. If you did, you'll need to pull the engine out again and replace it. The manifolds are up to you. I don't know your level of expertise. I wouldn't bother with the exhaust manifold unless you plan on putting on a high temp coating of some sort. Regular paint won't last 10 minutes.