I'd take clones before you initiate flower. Wait until you are certain that the clones survive and make it alive through their first transplant before flowering the donor. This is especially true if you don't clone very often, or haven't before. Then, you can decide whether to flower the CLONES or the DONORS. And that just depends on your space and grow style.
Another thing to remember is that removing the prime growing tips from a flowering plant hurts yield. You should only remove low branches if the donor is in flower, but low branches have low auxin levels and are very slow to 'take' compared to upper branches that get strong light.