4.6 Callaway engine in 4.6 HSE

I just picked up a 98 HSE with a bad motor on Thursday. I just picked up a 4.6 from a '99 Callaway today. I know the top end is different, but what do I need to run it? I snagged the engine ECU and MAF, but the air intake tube and airbox were broken in half and missing. I also grabbed the transmission and transfer case. Other than a broken battery cover, and a single lug nut pressed into the mud, thats all that was left. I know the TCU is specific to this transmission, but unless it is located on the tranny itself, I do not have it.

I guess my question is, can I use the stock air intake tube and air box from the 98 4.6? Is it worth taking out the working (apparently) transmission and t-case for the Callaway stuff?

Thanks in advance.