Hey bud, sorry, I meant to reply sooner after I saw this thread.......
I would NOT be afraid to take apart the master cylinder piston and clean it all spotless with brake cleaner. I do that allot and it can't hurt at all. Just clean it, blow it all out and put it back together with a bit of brake fluid on there.....
Unfortunately, thats the best you can do! I think the piston kit for that is discontinued but it may very well be still available or aftermarket too (hyperparts.com) That model may be rebuildable, I'm not sure but I'd check with Honda 1st, although I have had NO ISSUES with the aftermarket rebuild kits available...... They work fine for me 
As for bleeding, if it's pushing it thru, then the piston is doing something...... One thing to do is to remove that bleeder screw completely and check the 3 holes. The 2 side holes are tiny, it's the taper when the screw is tightened that prevents it all from leaking. But, the top hole is just as important as is the cavity the screw sits and bottoms into/on. I'm not sure if it's a "31 drill" but for some reason that comes to mind, but that can clean out the center hole. Then a teenie tiny drill does the 1 or 2 side holes and make sure it's all flushed out when done.
So many times when I have bled breaks I've forgotten to check them and they are usually filled with GUNK, WHITE STUFF and just corroded.............
Bleeders often crush those side holes if people over-tighten them.
Let us know what you find in there.........
(I'm having a beer for you right now
, Supercross is on SPEED channel right now.......)
P.S. - IDK where you can find it (Vets have it) but I use a large diameter syringe to pull and often PUSH fluid back up to the master cyl. to get most of the bubbles out. And both sides of that hose need a crush washer on there or air will seep in and fluid out!!
All our government does is distract us while they steal from us, misspend our tax $ and ruin our country