If you really want to spend money on a 253:
-Small cam. crow 5666 is about the biggest you should go on a relatively stock 253.
-quadrajet
-standard volume oil pump
-original hei ignition with the dizzy regraphed to suit the cam (easy to do yourself)
-extractors or stock manifolds, it won't really make a difference. If you're driving it on your p's, definitely go with stock cast manifolds. And a 2.5" single exhaust to avoid drawing attention to yourself.
-use the stock manifold or a performer. The egr cannot be connected to a performer so technically the car wouldn't be roadworthy.
-leave the emissions stuff there. None of it really has any effect at full throttle (low manifold vacuum) and increases fuel efficiency anyway.
Even after that, a standard vn-vy v6 commodore would blow the 253 out of the water.
As for the gearbox, if you don't have a supra 5 speed already with the shortened tailshaft, modified crossmember, bell-housing, yoke, clutch and speedo cable setup, it's not worth spending the money. I'd be going with an aussie 3 or 4 speed (m22 would be my pick with a shorter 1st and therefore reverse gear) because they're cheap to buy and easy to get parts for, if you're set on a manual. If funds allow I'd be looking at buying a 308 block and having it redrilled to turbo pattern and putting a t700 behind it.