I converted my 99-RT/10 to side-pipe exhaust using the factory Gen-1 sills. I originally used the dynomax mufflers, 3-inch straight through, 6 inches around. They fit fairly tight, but they do fit. (The bead on the end of the muffler touches against the side sill insulation in two small spots.) The only thing that may be different is the mounting. I had to use custom mounting, as mine is a Gen-2 without a side-pipe mount. I mention this because the six-inch muffler must be centered in the sill, as it is a tight fit.
P.S. I ended up changing mine over to the 2.5 inch straight through Dynomax muffler, 6-inch around, to make it even quieter. I also switched from Roe's oval cat to Roe's 2.5-inch round cat. It sounds allot quieter and I actually GAINED 8 RWHP. I was expecting to loose HP but I guess the header collector already necked down to 2.5 inches anyway. (It may have also been the cat as I have seen on this board that someone else picked up RWHP when they swapped out Roe's 6-inch cat. I like Roe's round cats much better for fit as the ovals touch the side sills.)
The current setup is a little louder that the stock side-pipe cars. Just loud enough to sound nice. It has a slight drone between 2-3k but not too bad.
P.S. If you are using an after market header, I would definitely recommend using the 3-inch in/out mufflers.
