Hello BLACKBEARD.
Welcome to the site.
There is a ton of great info and guys on this site.
One of the first things I would recommend you do is buy a Clymer Service manual.
There is more documented info in there then you could write about in a year, specs, pics, tolerances, ect.
What should I be looking for in this process? I guess I should drain the fluids and try to flush the bottom end thorally?
That certainly wouldn't hurt.
Since you have the top end off I would measure your connecting rod to crank side play with a feeler gauge.
From there it would all depend on what you find...