I had mine take a very long time, too. Did it during a record autumn drought, so every bit of humidity, I had to provide.
My setup was a big, Tupperware-like plastic box from Wal-Mart, with about a third of an inch of water in the bottom.
First, I'd put four flat rocks in the box, making sure that they would be big enough to stick up out of the water, once I poured that in. (For convenience's sake, I didn't put the water in until after I had the barrel in place.) I then took two thin sticks, and laid one between each pair of rocks. I then laid the barrel on the sticks, upside down, so that the dovetails from the front and rear sights rested on the sticks. That kept the barrel up off the bottom of the plastic box, and any discoloration would happen where the sights would cover it after they were installed.
I then put another rock or two in the box, and used those to support the tang and underbarrel rib.
I then gently poured a lot of warm water into the box, until I had about a third of an inch in there. Snapped the cover on, and firmly admonished the kids not to kick the box and knock the barrel into the water.
Like you, I had a lot of occasions where I'd get an uneven blued-and-rusted look--but eventually that gave way to a nice chocolate color.
I found that carding with a paper garbage bag scrap worked pretty well--it's a fairly rough paper, and did a good job on removing the rusty scale.
Toward the end, I used an old toothbrush and some baking-soda toothpaste for a semi-final scrub. That let me get into the nooks and crannies, and also helped deactivate the browning compound. Oh--for what it's worth, I'd expect the rusting / browning process might go on for a while even after you scrub it down pretty well with baking soda the first time or two. I had to do maybe three applications of baking soda solution to really finally kill off the browning / rusting process. When it stays smooth for a couple of days in a row after your last carding, you know you've stabilized it. Then you can apply oil, or whatever. Mine, I made a hook out of a coat hanger, ran that through the underbarrel lug, then put the whole thing into the oven on top of some aluminum foil, heated it to maybe 130 degrees, then hung it outside and applied a thin coat of pure tung oil. A couple of goes with that and it looks kind of like it's made out of dark chocolate. Nice, even, and smooth.
