If you need to make the bridge long enough that it would interfere with the mechanism, then sink it far enough below the talbe that your bridge will clear the motor or crank. A motorized version would be better since you wouldn't need to provide clearance for your hands to operate the crank. For your pit wall, check out a Micheals for embroidery hoops. If you get them the right size, you will have a nice round wall, so irregularities in your cut won't show. You can fill it with spackle. The bottom of your pit could be a false bottom above the Atlas turntable. Put a single rail around the perimiter of the pit to support the new bridge. The wheels will be hidden under the bridge, so you don't need to worry about how they look. I would get a pair of cheap Athearn or MDC trucks and cut one end off the truck so it only has 1 axle and the bolster mount. Then screw the trucks to the bottom of the bridge so that the outside wheel is supported by the rail in the pit. Get some square styrene tubing in 2 sizes, one to fit just inside the other. You can build the bridge out of Atlas flat car load girders. Make a box out of the thickest styrene you can buy at the hobby shop for strength, and make a square hole in the center of the box to mount the larger of the two square drives in. Solder one wire to each rail on the Atlas turntable and make them long enough to run up through the center of the drive square, through the smaller drive square on the bridge, and solder to the two rails on the bridge. Again glue a piece of styrene to the bottom of the bridge, and drill a hole dead center on the bridge and file it to fit the smaller square tube. When you slide the bridge square tube into the base square tube, you will have a drive to transfer the rotation from the Atlas table to the new custom bridge. The power will transfer from the Atlas tracks to the new bridge tracks. The hole in the floor of the pit for the drive to go through should be bigger than the drive squares, but small enough to be hidden by your custom bridge.