hydraulic question

I've been lurking here for a couple of years. During that time, I've picked up lots more information than I can handle.

I have a 1980 White-Iseki 2-62. Don't throw rocks; it's not what I wanted for a tractor, but the price was right. My FiL bought it new with a Westendorf WL22 loader. After he passed on in 2002, and MiL sold the farm in 2004, the orphan just found a home here.

Anyway, the loader right side hydraulic cylinder blew out its seal. The fluid was milky, so I knew right away from reading posts here there was water in the system. I have drained the transmission, replaced all hydraulic hoses (16), and have a new suction filter for the transmission.

My question: I know everything has been drained. There is probably some water still in there. Will it hurt? Should I run it a bit, and drain it again, or what?

Any help will be appreciated.

This tractor was always shedded when the FiL had it. I don"t have that luxury at this time. It appears somehow the original fill plug on top of the transmission got lost, and was replaced with a plug that kinda sorta fit. I try to keep a tarp over it, but got a little lax on that last summer. I have replaced the plug with one that fits.