Excuse me if I am not fully understanding your problem. You have a stock frame with the rad support bolted to it and the inner fenders don't reach between the rad support that is bolted to the stock frame and the body that is bolted it as well? The only issue could be the inner fender being bent to clear your suspension or something like that which would effectively "shorten" the inner fender. That is the only thing that makes sense.
Does the inner fender need to be trimmed to clear the new suspension?
If it has a frame clip on it where the front of the frame is different, then the rad support is simply mounted too far forward.