Thanks to all that replied to my question. You were all very helpful. I think that i will just keep hitting the shiftter too. I am getting a new civic in February, maybe it will hold out until then. Nothing else seems wrong with the car other than having an anoying cv joint going out. But I have drove on them busted for months. I might fix it but i doubt it. It's not bad yet.
This next honda i get will definatly be a standard. Then I can't have this problem again.

Thanks everyone,
Jaden