I've heard stories of people removing the trans with the Y-pipe in, but I think their memory is bad.
It's a million times easier to just remove the Y-pipe. It can be a bear to break the manifold to Y-pipe bolts loose for the first time, but use a wire brush to clean up the threads that are sticking out before they go through the manifold threads when backing out, and it's a lot easier. I'd also suggest just buying 4 new bolts from Ford to replace them, it's a lot easier and the Y-pipe will seal a lot better, most of the time the threads that were in the manifold are rusted bad.
You can pull the Y-pipe together with the catalytic converters, just disconnect the cat/muffler spring bolts and drop the Y-pipe together with the converters to make it easier.