auto - manual conversion has been done in so many vehicles it shouldn't be any different in ours. Bell Housing, clutch + res(Not sure if it's a hydraulic clutch), tranny, pedals. I'd love to swap a 6spd into my truck but I can't afford to have it off the road for a few days while I do it.

 

I had exactly the same thing in my 05. Turned out it was the lockup Torque Converter throwing a temper tantrum. Took it to the local AAMCO egghead, and he changed the filter, and also put in an additive that actually fixed the problem. Now it runs great.