Yep, the CAI will swap right over. Externally, the engines are identical, all of your parts and accessories will swap right over. Personally, I'd try to find a relatively low mileage 6.0 and bolt it in and run with it. At least with the prices of machine shops around here, a good rebuild will get rather pricey, and there will be a lot more down time. My 03 LQ9 shortblock has 27k on it and the cylinder walls look brand new...it helps that the original owner maintained it well too.

 

Thanks for the feedback. I think this is the path I will probably go. Step one is to find and purchase a motor. Once I have possession of it I will start collecting the parts and accessories that are going on it and once I have everything it will time to swap.
I talked to a local transmission shop that has been highly recommended by some guys around here and they said they could rebuild my 60E to handle the new motor for a decent price. One question I should have asked them was would it be a good idea to have the tranny rebuilt and beefed up to handle the 6.0 and just bolt it back up to the 5.3 until I am ready to swap? What do you think?
Here is the tranny shop I was referring to....
http://www.texasperformancetransmissions.com/2.html