I didn't touch anything relating to air conditioning system.
There is no need to cut any parts of the body - except on coolers where you have an outlet / inlet on either side and you want to take piping up on drivers side of engine bay, whereby you have to cut a hole to accommodate piping under battery area. Thankfully there is a preprinted circle where to cut this hole - apparently due to fact that if your car's body was destined to become a gtr on production line then this is where they would cut - but if your car's a gtst etc then the perforation, but no hole, exists.
I don't think the 180 degree turn will be an issue for you. In fact i think its Blitz that make skyline coolers in this maner. Not perfect but still very good.