Edit: Revised topic title, I'll use this post to chronicle my progress.
Got the y-pipe off this weekend and dropped the transmission pan. Transmission fluid looks good, no metal shavings or gunk in the pan. Replaced the filter and got everything bolted up in place and topped up with fresh ATF.
Y-pipe has some horrible welds on it and lots of dents. The muffler is blown open and the exhaust pipe from the muffler back looks like swiss cheese, so that's all coming out. One of the studs on the manifold that the y-pipe connects to is bent out so the two studs are kind of like a V, makes it really hard to get the flange off. Not sure how that could happen?
Will need to get some new exhaust installed, was thinking of picking up the Hedman Headers from BJ's, but I saw a post alluding to discussion on the forum that the stock manifolds are preferable? I couldn't find any threads explaining this....