Cyclonite,
First off if you only have two I would suggest not totally re vegging either plant but as you said just taking a few clones from it. It really shouldn't stress the plants. When you do take them I would put them under 24hr fluorescents until they root. Put them in a small dome and spray them twice a day for the first week and then once until you find they root. As far as re vegging the ones that are getting close to finished, you could give it a try but I'll tell you I haven't had much luck with them surviving after you've chopped them to almost nothing. Just keep good track of which starts came from which plants and over a short period of time/harvests you'll know where the strongest buds or highest yields (hopfully the same plant) came from. At that point you can finally get down to just the mother you want to take starts off from that point on. Good luck and I hope this helps. Of course all I've said is just the way I've done things. Oh yeah and I use rockwool cubes to do my starts.