In my case clean out proved to be a big job. I tried buying cheap oil, and replacing oil and filters repeatedly. Water was always hiding. Brakes would freeze up in winter. I ended up taking it to Reed's in Claremont NH. They went through the system cleaning one component at a time. Ultimately, I needed a new hydraulic pump. Now it's a very nice tractor. I spent more on it than I would have chosen to.
Willie
I ended up taking the rod over to Mooradian's Hydraulics over in Castleton, NY just south of Albany yesterday Willie. It's a bit of a hike, but there's a good reason why I did it.
2 years ago I purchased all the parts to build a wetline for one of my tractors. They stock everything imaginable. Then one of the 2 PTO's I had on that truck started leaking, so I brought it back to them to re-seal it. Long story short, 6 months passes and they lost my PTO...vanished. They tried to make it right by giving me another one...but I dropped off a Muncie, and they gave me a Chelsea (which is actually better,) but the gears were nowhere near the same as what I needed to work on my transmission. So instead of getting all upset and mad, I figured that this might be a good opportunity to get evened back up again. They are a full-blown hydraulic cylinder rebuilding shop too which I didn't even realize until I called them this week, so I ran it over there yesterday. Me and one of the guys in the shop immediately went to work on it removing the nut and piston off the rod, and if the welder wasn't out sick, I could have had that thing done in an hour he said.
So I have to drive a little bit for this, but the end result will be a new rod for literally nothing in exchange for my misfortune with the missing PTO. It was 2 hours to Castleton, NY.... or 1.75 hrs. to NH Hydraulics in Merrimack, so not a huge difference. Should be all done tomorrow morning he said. That's a bit quicker than the other cylinder I had done at NH Hydraulics after 2 weeks in their shop.
I'm going to try and flush the system as you said with Tractor Supply oil and filter a couple of times to see if it clears up, but like you say, water seems to find those low spots and it's tough to get it all. Good news is I'll be very, very careful from now on below freezing.