engine rebuild and torque question

What's your clearance read on the plastigage? Maybe you have the wrong bearings.

My 02 GT shop manual says the main caps should be tightened to 30 ft-lbs and then an additional 85-95-degrees. What reference are you using that says 20 ft-lbs + 90-degrees?

For the rod bolts it says 18 ft-lbs (stg 1), then 30 ft-lbs (stg 2) followed by 90-degrees.

You should install one piston/rod assembly at a time and check for rotational issues.

It sounds like you've clearly got one or more rod bearings that have insufficient oil clearance. I'd beg, borrow or steal a bore gauge and micrometer to measure the crank journal and bearing bore diameters to determine your oil clearance.

BTW, the rod bolts should be replaced. They are torque-to-yield and stretch and permanently deform on that 90-degree tightening. If you re-use them, you'll weaken them and risk a bolt failure down the road. Every time a TTY bolt is stretched it should be replaced.