I would prefer to see the pics before commenting, but without em, I can say thats prob normal territory that comes with the transplant. I wouldnt get worried unless it doesnt seem to look better over the weekend. Whats the humidity like in that room? is it warm enough for them? They prob could use a bit of warm temps and the light very close to them since its a CFL (im hoping the bulb is not especially hot - If it is, keep it a bit away of course, but normally CFL's are cooler compared with HPS). You may wanna forget about the fan until the shock has worn off and you start to see the branches "reach" towards the light rather than droop. Once theyre strenghtened up again, reintroducing the fan to strengthen wont be a problem. You'll have quite some time in between then and flowering for them to get stronger.
I wouldn't cut them out just yet unless they are really blocking any important bud sites or anything. You said that they are on the lower sets anyways, and thats likely because the light isnt reaching them in the quantities it would like right now. Did you happen to add the mylar/blanket/white paint to the room? It might not be something you can or would wanna do, but if you have cool flouros (tubes) or even the bulbs you veggd with, that you could position around those areas that are drooping, as long as you still have your flowering bulb on and are doing the flowering light schedule, i dont think it'll revert your plant into a veg state, but it'll give the lower sites some strength.
Hope this helps, and anyone who has more that they can add, or if you disagree please point it out so this guy gets the right info..