I am not sure what you mean about outlet pipes being on the wrong side.
I just had a look at the rads off my 01 CR500 and they look exactly the same as yours.
Except for the small hose that joins the top of the 2 rads together, your hose goes back and around, where as mine goes forward and through a hole in the frame.
You didn't happen to put the left on the right and the right on the left did you.

I just took another look at mine, if you are talking about the little cross over hose outlets.
They should clear without any problems as the hose goes under the front of the fuel tank, the outlets tubes should be no where near the tank /HEAPS OF CLEARANCE!
