EDIT, Sorry, not patient enough to read one giant block of text today. I see you've checked most of what I listed. I'll reread it later and see if anything else comes to mind. You have a thermostat on the cooler? and is it a full flow cooler setup or bypass?
Your issues are unique... most people track down and fix the real problem by set number two.
Seriously though, people make a LOT more power than you're seeing and use the stock pump without issue. Some shim the relief valve for a pressure bump but it's not so common any more (just one of those things which everyone recommended until someone actually researched the oil system and found it sufficient to support 700RWHP... ya know?)
Have you replaced the pump? The oil squirters? Pulled the pistons and made sure they're sound? Checked that the cylinder bores are true? Have you measured the crank to ensure that it's straight? If it's been pulled and improperly stored without supports it may warp from its own weight. Have you measured the journals on the crank and the rods to make sure they're true and really round? Measure the rods with the caps bolted and torqued. Have you made sure the oil inlets/feeds in the rods and bearings are unobstructed? There's a lot of stuff which could contribute to your problem. I'd start with what's mentioned... if the pump hasn't been replaced I recommend you replace it; make sure the replacement is for the GTE and NOT GE. Replace the oil squirters.... they're essentially a controlled leak and can open up at too low of a pressure over time... same for the stock POS oil cooler setup actually (You ARE running an oil cooler, correct?).
400 at the wheels is about the limit for a
healthy GTE (rebuilt, it actually take more but requires upgrades apart from the long block). If you picked up a used engine from Joe Blow then you can only guess what you're going to get. You see very little complaint about rod knock with these engines given the age and amount of abuse they usually see; See it more with JDM engines or domestic if they've been sitting in someone's yard.