I agree with kevin95695, Joes Juice works very well, and it would be much easier to zap them before you started aquascaping. then add a couple of Peppermint shrimp to take care of any you don't find down line.
As for the inability to use a bulkhead there, shouldn't cause any trouble. I don't know about spaflex, but I did the same with pvc on my 60g. Just ran is through the hole and connected an elbow on the end of the pipe just under the waterline. Looking good so far.