This is how I like to do it, and since you have fresh rebuilds on your lift cylinders, it's all good.
Warm up the machine, get it to where it can set awhile and raise the boom all the way up to the stops. Put a boom stop in for safety, but don't lower the boom onto it.
Remove the left motor cover between the wheels, and disconnect the case drain line from the motor. This will drain the tank. It's a little slow, but it's about the lowest spot in the system.
Remove the hydraulic filter. When it stops draining, remove the boomstop(if the boom hasn't drifted down onto it) and let the boom down to about a foot off the ground without starting the engine. Get out and disconnect the tilt cyliner lines and move the bob-tach back and forth by hand. A helper with a bucket helps to contain messes here.
Hook the tilt cylinder lines back up, get back in and let the boom all the way down. Then let it drain some more. You can go into the other motor and drain it, too.
When it stops draining, hook everything back up, install a new filter, and add 5 gallons of oil, take it out and run it for a bit, then do that whole thing again.
I usually do this twice to turn milky oil clear. The most I ever had to do was three times, but I had to do it on three different ocassions until I found the machine had a hidden hairline crack in the hydraulic tank.
The point is, try and find out how your water got in there also.
Some folks will tell you to pump it out the aux, but I'm always skeert to run the pumps dry, even for a few seconds.
Good Luck