Ideally when her litter is weaned off at 3 weeks old1: When can my female breed after birth? I know right away, but ideally how long should I wait her out?
Yes but I don't recommend it for 2 reasons, possible aggression and back to back breeding which take a toll on the females, and lead to smaller litters and babies as they nurse while pregnant.2: Can the male rat safely be left in with the female and her babies? (so say in the event my girl gives birth over night and the male is still in there)
For male cage mate see answer above.3: Should the female always be housed away from her future cage mate after birth to prevent the other rat from attacking the babies? How common is that?
For female cage mate you will experience loss as the females will fight over the babies, I recommend communal nursing when babies are at least 5 to 7 days as their skin is less tender, until than I recommend individual birthing.