Ok, I feel dumb and annoyed at the same time. The problem was that the 3/4" nut that comes through in the middle of the top hat was only finger tight. I hadn't thought to check it as everything I'd read pointed to the bottom bolt. Anyway, just for kicks I tried to wiggle it and low and behold, it was really loose. So, I feel like an idiot for not realizing that in the first place, but am rather angry at the fact that i paid a shop to fix this and they didn't tighten up one of probably 5 visible bolts. Granted, they did do the half-assed fix on the bottom, but still... Either way, i just tightened it down with a 3/4" socket and the thunk is gone and the car drives perfectly. The shop will get a piece of my mind for causing a week and a half of annoyace though. Kind of makes me wonder what bolts might not have been tightened down when they did my head gaskets, radiator and power steering pump too.
