VVT delete if you don't want that. But think most are keeping it unless going all out like silver sleeper kept VVT for along while now he's turbo'd tho and built so may have had all that stuff deleted when he sent the engine if to be built. Only thing I would personally change in it is nothing! But then again if the money isn't problem cam and VVT delete would be a great opinion. Allen can spec you a cam and sent you a harness and tune so you'll be ready to go when it's ready and all buttoned up.

As far as transmission you may be able to find a 2wd trans straight trade so you aren't ripping apart the tail shaft just to change it. Also I think the computer is in those transmissions so don't fully know it's it would be a good thing to convert to 2wd. Although I'm sure it's been done cause these setups are a dime a dozen now. Best thing to do is just forward your whole message to Ray or Allen they will give you solid transmission advice.