I just went through a similar problem flushing out debris after I trashed a part internal to the transmission. I bought a gallon can of WD40 and put it in a spray bottle like for cleaning windows and used that to wash and flush everything to the bottom where I could drain it or wipe it out on the side of the case I had opened up. I didn't feel good using any kind of solvent because it takes the oil film off things like bearings. Sounds like your situation is a little harder to get the fluid out, maybe use a vacuum oil change hose or a turkey baster with a piece of tubing on the end to reach those hard to get at spots. A magnet might also help to get out little pieces.Anyone have any suggestions on how to best clean the tank out? I'm thinking that I need to get some solvent in there to clean out the oil, then I can probably get a vacuum hose in there at least on the side where the filter mounts, and maybe blast some compressed air in the other side with hopes of stirring things up enough so it ultimately gets sucked out by the vacuum.
Any other ideas?
You could send some of that hydraulic fluid into Blackstone labs (if you still have it), they will tell you what kind of metal contamination is in it. Might help diagnose the original problem.