Finally got around to properly installing the new master cylinder and bleeding the lines. Had some trouble introducing brake fluid into the new system but I sort of figured it out eventually. I ended up reverse bleeding the line to force fluid into the mc when my hose popped off...
The brakes are still super spongy and pretty much ineffective but at least there's pressure now. I'm just going to finish up with the rest of the bike and then come back to it. I'm sure there's just a ton of air cached away in little places.