If it was running fine when pulled, I wouldn't worry about pulling the head, unless you plan on doing a valve job on it. Do you know the milage on it since the "rebuild"?
The head bolts shouldn't need replacing. If they hold the 90 ft/lbs. when reinstalling the head, then they are fine...
It won't hurt to replace the pumps, But if the rear main isn't leaking, then I wouldn't screw with it, you could just make it worse...
If this engine has the special drilled head bolt, it should have an "O" marked on the top of the head, and it should be located in the middle passenger side of the head. This bolt is only necessary on 59-62 blocks with the older center groove rocker arms (53-58) and If the block passageway has been pluged (in order to force the oil through this bolt). If the block hasn't been plugged, then the bolt serves no purpose. If its there, then just leave it in.
FYI...
If you are using a 59-62 block, then use 59-62 rocker arms with the offset oiling grooves. If you do this, then there is no need for this special bolt.
53-57 blocks can use either type of arms without any issues.
All 53-62 heads are interchangeable. AGAIN, the issue is NOT the cylinder head, its the combination of blocks and rocker arms that is the real issue.
