Here is a bit of follow-up. Latest gas mileage check was 14 mpg (highway). New composite gaskets and D2 style bolts with spacers are working great.

The answer to the initial question about the Y-pipe: only needed to disconnect the joint before the muffler. That said, the hardest part of the job was aligning the left side manifold bolts, using a floor jack and pry bars to get the angle just right. The bolt on the back end was very challenging, needing a tap to correct a little cross-threading. If I had the manifold out, I would have enlarged that hole a tiny bit.