Yes, used a 20mm hone (the kind with the abrasive balls) ... but that's a good point about fluid moving from chamber to chamber, didn't realize that.
But it's moot, now. I broke down and went out and bought a new Aisin T100 MC according to this write-up:
Toyota Land Cruiser Brake Master Replacement and Upgrade- ORN
I've run out of other things to try.
For anyone else looking for what MC to buy, I got Toyota part # 47201-3D020 which also corresponds to 1986 + V6 truck. I got the one for the T100 because you can splice in the level sensor to work with the FJ60.