Sorry to hear about that. Breeding animals results in this type of thing once in awhile. I've lost a few breeders too.
1. You can. He might try to breed with her but usually she fends him off. I did have one female bite the heck out of one of my breeder males for pestering her. I usually pull my females a few days before they birth.
2. That is up to you. I give them a rest sometimes if I have tub space or they have had several litters in fairly rapid succession. I don't always give a resting period. The younger the female the better chance you have to produce repeated back to back litters.
3. All my adults (breeders) get scraps, stale bread, stale crackers, cheerios, and even meats. I'm a pretty firm believer that healthy rats produce healthy food. This isn't necessary if you're feeding a high quality lab block but the extra fat and calories can never hurt. I almost always make sure pregnant or nursing rats get the most treats.
4. Some traits are dominant or recessive just like snakes. It has nothing to do with the sex of the animal as far as I'm aware. The brown might be recessive so you won't see it until you produce and hold back a male that carries the gene.
Regards,
B