Final case/trans is the oil supply point, the under seat stick will be the one for level.  You will want to see it fairly high on the stick before startup as considerable oil drains back when shut down, running level is checked at temp in neutral.  Will be a scavenge/supply pump on the tractor, usually engine or torque converter flywheel driven so the engine can power up the hydraulics, if the line changed is for the suction there it could be sucking air there, I had that happen with a brand new hydraulic line on my scavenge/supply pump for my power shift 7G.

Screens are really fine mesh on these, takes considerable materials to stop one up but they will stop up.  I would consider drain off old oil, pull and clean screen(s), replace filter(s) install correct weight oil to the refill quantity on data tag or manual and try it.

The pump on the converter housing is shaft driven from the flywheel side of the converter, there should be a larger diameter hose from the trans sump area and smaller high pressure hose to the feed block of the trans.  Larger diameter hose cannot have kinks, rub throughs or soft spots and behind the sump fitting there should be a removable strainer, on mine is a four bolt block that removes. The high pressure line should feed thru a filter then to controls system and feeds into trans.

Will need to get on Minnpars web site and look up your machine to determine how much is still available internal to trans.  They are a beast to get into but are workable provided parts still out there.