I'd run the 3208 until it was junk, then swap in the 3408. Those 3208's will be underpowered compared to what you want, but you're on an IDI forum, so you likely know all about that. You can boost them, but it only hurts reliability. IMO they were marginally better then the 8.2 detroit, but worse then the 9.0 IHC. They were made for a good while so you might still be able to find cheap parts for them.
Swapping though, you might run into a problem with the width of the 3408. IIRC one of the big makers had to do some monkey business with the frame to get their engine to fit(might have been mack now that I think of it.)
I was told the 3408 was good, as was the mack E9, but to run from the VT555 cummins.