the sides on my TD extended down past the floor, as well, about 1/4 inch. after I flipped the TD over to glass the bottom, I used my small circular saw to shave off the 1/4″ excess. then that provided a flat surface to run my router on.
when I was anticipating cutting the hatches and doors out of the TD, I looked around for a small circular saw that was easy to handle with one hand, and one that I could easily see the blade and the cut line. I ended up with the Dremel Ultra-Saw. about $100 at Home Depot. it comes with 4 blades, one of which is a fine-tooth wood blade which worked great. it is small enough that I could rest the front end of the foot on the cut line, then slowly plunge the blade exactly on the cut line. thanks to the fine-tooth blade and the fiberglass/epoxy on the shell, there was no chip-out.
for trimming the 1/4″ extra from the sides, I marked a cut line with a sharpie. I left the sides just a slight amount proud and finished it flush with my orbital sander.