If you are not holding down the clutch during stops, or have a worn transmission input shaft bearing (inside the transmission), another possibility is that the transmission is not centered perfectly. You can leave the bellhousing on the engine without the transmission, attach a dial indicator to the crankshaft, and turn the crank while the indicator tip rides on the transmission indicating hole. If the hole isn't centered, you will have to remove the locating dowels and shift the bellhousing slightly to get the runout as close to zero as possible. I like to get it under . 003". The best approach would be to use a center punch to egg shape the dowels slightly and use a Dremel to open the bellhousing holes in the direction needed so it ends up being centered correctly by the modified dowel tubes.