ab,
I have a fluidyne "stacker" system that fits in the stock opening. It is similar to that seen on this page:
http://www.fluidyne.com/pl_radiators.html
called the Double 38mm with stack EOC.
What I did is sent them the dimensions of the radiator opening and size and location of the fittings/hoses and they custom built it to fit. The EOC (engine oil cooler) is slightly narrower than the radiator as the stock opening on the VIper is as such. Let them know your intended use, HP level, etc. and they will size the number of rows (thickness) accordingly. This is a nice set up becuase the radiator and oil cooler are in parallel and get clean air as opposed to a stock set up in series where some of the radiator air has already been preheated by going through the oil cooler.
I have a H M S carbon air box that fits fine. I have not tried a stock air box.
Cost custom sized with all the proper hose/fittings sizes for the radiator and oil cooler was just under $1000 directly from Fluidyne.
I have a fair amount of HP, a stock hood (no center vents) and raod race in high heat (THill,Buttonwillow in summer) and have never had high temp problems with this set up.
I also have dual fans that I wired to the stock plug/sensors.
If you are interested further, I can take a photo and do some measurements for you.
As a side note, this is the same set up used on the ORECA cars, only not as thick.
Regards,