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.