Tim,

Sorry about the slow reply. Been pretty busy.

1. there is a restrictor disc that goes under the needle in the center of the filter base. They have been known to come out and then you will get oil pressure like you have.  They don't have a call out for just the disc in my parts book.

2. The paint changing color on the manifold sounds normal to me. The center is where the heat from all 6 cylinders collects, and so the manifold is hotter there. It will eventually burn it all off, but #1 is the coolest.

3.  The top bearing in the front of PTO clutch goes through the PTO housing and the rear end. If you had the PTO gearbox off, and then put it back on without the PTO clutch in, the hole might not be lined up. You'll need to loosen the PTO gear box and get it so that the front PTO clutch bearing goes into the hole on the tractor rear frame before tightening the PTO gearbox back down. If the holes aren't lined up, it puts a tremendous thrust strain on that bearing, and it will fail in a very short time. I made this same mistake on my 660, and had to put a new bearing in it. 

As long as the shim stacks are all equal in the PTO, I don't see why it would whine.

Let me know what you find.