I'm thinking when your fluid gets hot, your FEL problems may return. Now, I'd also raise the FEL and then shut off the engine. If you have a load in the bucket, it would be better. See if and how long it takes for the FEL to drop from the raised position. If it holds or drops very slowly (a few inches over 15 to 20 minutes) your FEL is normal.
I think both the main hydraulic filter and the HST filter should be changed. Also, with the tractor running, squirt some oil around that rubber "T" in the line to see if it gets sucked in between the "T" and the pipe where it is clamped. You may have a little air leak there. I don't know how many hours you have on your hydraulic fluid, but NH suggests a change at 300 hours. I've looked at my oil and it is crystal clear at 300 hours so I let it go to 500. I do change filters regularly. The HST filter on the left side of the engine is the most important. If your FEL works fine, the main filter is probably okay, but you may want to change it just for 'insurance' that both are okay. I recommend using NH filters for both of these. NH filters are more expensive, but you always know you have a filter that is proper for your tractor. To me, that's worth the extra money. The big expense to operating a tractor is fuel anyhow. Compared to 20 gallons of fuel, the filters are cheap.
BTW: Your HST has test ports for pressure testing. They are under the seat where there is an access panel. Your dealer should have a full test set to check the bypass pressures on your HST. If they are at 5000 psi, then your HST should be healthy. To test the charge pump, they have to modify the assembly above the HST filter so an adapter can be added to check charge pump pressure. Both of those tests will probably be good things to have done at the dealer. By the time you buy all the fittings, gages, and hoses to do these tests, you'll have spent more than the dealer will charge to do the tests.