Yes, you will have problems if you rotate females around. If you want to have 6 females, get 2 males, and just have two colonies...1.3 and 1.3. this way, the Males and females will know each other and you won't loose time while they get to know each other after every 2 kits.
Rats and mice don't seem to have problems when you take away their offspring. I have been told that rats lactate pretty much all the time...When you go to a pet store to buy feeders, pretty much all feeders that are still nursing are nursing on rat mothers. Also, Female rats will help eachother out with the nursing while there are babies around. Kind of funny. My mice do the same thing.
If I were you, and you want to stock your freezer, I would take all but 2 or 3 pups from the litter the day or day after they are born. This way, the mother will be more likely to produce again sooner.
I wouldn't interbreed rats or mice as I have heard of some problems with this. Do a search on it. I know that there is a thread in the feeders forum that talks about this.
Hope that there are more people that come around and help you out.