I'm a fan of not adding unfiltered oil to motors. I saw a report once on how much debris on average is actually in a new can of oil, and it put me off the habit. (I do fill filters, but only in the direction of the oil, never any dirty oil on the "wrong" side of the filter. Things may have improved in the last decade, but if it were me, I would pass on adding oil.
I would clean off all of the motor fittings and the entire area round the motor that you might touch (power wash, blow off with air, then repeat cleaning with brake cleaner, wipe with clean towels and repeat until no more dirt appears, then open the threads a little and repeat the brake cleaner). Terry once commented that working on motors needed to be heart surgery clean because anything that gets in to the motor is recirculated for a long time in the motor circuit. The advice stuck with me.
I bought a nice set of JIC metal plugs off of Amazon, that I find quite useful for sealing loose hydraulic hoses ends as soon as they come off, unless the hose is going on the next item immediately. Personally, I prefer to transfer the hoses one at a time as I loosen one hose from the old motor, remove the hose, and move it to the new motor. Fewer opportunities for me to do something dumb like swapping hoses onto different ports. Labeling the hoses before you start helps, too.
Once you power the tractor up, the motor pressure will basically go from 15psi to 3000psi as soon as you pressurize the motor, and the air volume will collapse to a tiny fraction of itself, (0.5%) and as oil bleeds out of the motor system, the dissolved air will be carried off to the tank. The air in the motor circuit may/will make the motor response "spongey" for a little while, so my two cents is to plan your stops with lots of room for delayed response until you get the hang of the delay in the pedal response. It gets better with motor use; in my experience, pretty quickly.
All the best,
Peter