I know that all sounds a little complicated so basically, heres my plan: I would just have 1 breeding pair to start, and once they had one litter, I would remove the male. Once the babies were weened, I would separate them according to sex. I would then take care of them until they are all adults. (throughout this time I will continue to purchase feeders from the pet store). Once I am down to a certain number of mice I will allow one more litter to be born, and start the process over again. Hows that sound?
Really the only thing I'd be concerned with is this, you say you would remove the male? Would you be feeding him off then? I would recommend that you do, because if you were planning on holding him seperate from the females and then adding him back for breeding later, you may run into problems. He may not be re-accepted by the females if he's been gone too long. If it were me, I'd start my next breeding group with the babies you are raising up.