I don't know WTF you're talking about, about the "click click".
In any case, stick with the auto and call it a day. It will cost you a buttload to transfer it to a manual and it's not really worth it.

You're better off building up the engine and doing tranny upgrades and making a faster automatic car.

Either that, or go buy a new car.
I s'pose you could find the tranny (if you're planning to boost, stick with an LS tranny, if you are going NA, go with an ITR tranny) in a junkyard and then provide the parts to the shop, that should cut costs a little, but not much.