That boot is just a dust seal of sorts, the seal on the plunger is what's supposed to hold the fluid in.
This is all too common I'm afraid. The potmetal these are cast from is prone to pitting and I've had a #$%* of a time getting them to reseal too. Some guys wrap wet/dry paper around a dowel, wet it with brake fluid and very lightly sand the bore of the MC to try and smooth out imperfections. I bought a set of lightly abrasive rotary brushes and used them in my cordless drill to polish them up with that - that has worked a few times, but not 100%. Whatever you try, yes the entire thing has to be disassembled, and then all the parts very carefully cleaned with soap and lots of water to get any dried crystalized spooge out of the system, including the reservoir. Then rebuild it again, keeping super-clean, using fresh brake fluid for lubrication on the new seals and in the bore.
If that still doesn't work then your options are to scrounge another, or to possibly get yours resleeved. I had to send one to a place called Apple Hydraulics, and they inserted a nice bronze sleeve (for ~$100 as I recall) and it sealed up perfectly, and is likely to now be rebuildable to infinity and beyond. They also nicked and scratched up the exterior of it pretty badly, so be prepared for that if you use them - you're going to want to powderblast and repaint it when they're through.
