Yap. I beleive you can even use the newer oval-port heads from a 3L and use the SVT cams in them without modification. Your style fuel system only determins the LIM you'll use, or more specifically, the kind of injectors you use with your LIM.
My car has return-style fuel system and I grabbed up a top-feed fuel rail and SVT LIM and picked up the matching orange top-fed 19# injectors from a 98 SVT. Car runs SWEET.
I was in the a similar situation as you. I thought I had rod knock in my 2.5, and knew the motor had to be replaced. A new 3L shortblock from Bill J was so much cheaper than replacing it with another 2.5L. Of course, after all the upgrades that I got with it the cost was about the same as a 2.5L swap, but I have a much faster/fun car though. You can even do it really cheap if you wanted, using your 2.5L heads and cams and stock fuel system if you absolutely had to
