[Wisconsin_Snake]

Welcome... At the rate I am going you'll probably complete your kit before I do mine. lol

Pedal upgrade, I wish I went the route of a hydraulic clutch vs the cable. From what I have seen get the Wilwood pedal for brakes and clutch where the pedal hang down and the MC face forward.

Trans mount is super easy... The cross mount is a flat bar that goes strait across across the frame. I used a 2x4 during mock up... The same cross is used from auto / manual transmission. (If I understood your question correctly).

The heater box was made by CR but it bulky. I better option would be to buy a small heater box and run tubes to the vent locations. ie "Vintage Air 506101"

Side pipes you are going to have probably get made.. The CR ones were REALLY restrictive and most people swapped them.

If you search the CR2 forum you will find specs for getting the CR rollbar.
Use that to have someone create you a set. Other roller bars will most likely not fit/work with this body. (If you search my user name I tried to do a group buy but never got enough people but the spec sheet should be in the thread).

Post some pics of your kit when you get a chance.