I just spoke with D&D to order my replacement motor. While I didn't ask about your motor specifically he did say that the comm bars lifting on my motor were due to heat damage from earlier in its life. You can read my post here: http://www.diyelectriccar.com/forums...7&postcount=14
Basically a normal D&D motor can safely go up to 6000rpm. Mine only went to about 5500 rpm. Given your motor has overheated way more than mine you probably want to keep it below 5000rpm. In any case, this shows that you can shift way later than my might have been. Leave it in a lower gear. As David suggested above, you should really consider forced air cooling. D&D does sell the band which goes around the brush end for $55. That is less than I spent building my own.
Another thing to consider is to go with an 8-brush design if your motor doesn't already have 8 brushes. In any case, you might want to contact D&D and talk to one of their engineers about what you can do. They are in NY so you may have a bit of shipping cost to return your motor for a rebuild but it might be worth it. D&D's website is http://www.ddmotorsystems.com/
but you should just call them. They prefer to talk over the phone and are very helpful.