Something is clearly wrong, and until it is found you will continue to chase your tail, so let's see if we can stop that time wasting.
When you ran the tractor most recently and it boiled over, are we talking about the radiator boiled over and the tractor overheated? In what timeframe are we talking about that 'this' happened?
Here's what I might do. My thinking is to go down the line, one item at a time, starting with the most likely, and possibly easiest first, to see if change can be accomplished. We don't know what effect the 10 Micron filter is having on the circuit. To my knowledge 10 micron filters are fine for fluids like diesel or gas; not sure that hydraulic fluid can pass through fast enough to not cause problems like you have. Remove it and see what changes, if anything. Report result(s).
Is there anyway to determine where this pump is SUPPOSED to be mounted? Have you reached out to the Yanmar forum(s) guys to see if anyone has this pump on their tractor, and if it's mounted on front shaft or rear PTO? Is there a part # or anything at all to identify this pump?
Maybe a close inspection of the pump would show an arrow or some markings that indicate direction of intended flow.
I like the idea of using grease to find the suction (leak) point(s). And I really like the reversing of the fittings on the pump to hopefully get the flow of hydraulic fluid less restricted, and possibly solve the squealing, etc., BUT I wouldn't go to that effort until some of the other possibilities are explored.
If you don't have colored tape mark them with whatever you have and code them with magic markers or cable ties or similar.
Here's a link to a good explanation,IMHO, of what and where filters are to be mounted in a hydraulic system. Read through all the types and what it says about where they need to be mounted in relation to the tank and restrictive valves. (It's from the EU, but still applies to your situation).
Hydraulic Filters: Return Filter, Pressure Filter, Suction Filters, Parker Parfit Replacement Filters