I found a low compression rebuilt marine long block for 3500.00 or a rebuilt long block for 3000. I want to take advantage of running the low compression and higher boost but would it be worth it? WHat would u guys take as an option. both motors carry the same warrenty and such.

You'd have to put the timing cover, and HB from the '98 for the CPS to have a place.

IMHO, the high compression ratio of these engines is their achilles heel, well that and the IDI pre-cup injection set up. Dropping compression not only allows you to run more boost, it really helps bring this engine to a more comparable level to other diesels available. It also lowers the amount of energy used up to compress the air on each power stroke, less resistance = more power. Its got to be easier on the pistons and crank too, I see no reason why it wouldn't improve longevity and performance.
Really the only downside is startability. It shouldn't be that big of a deal with a fresh engine, but I've heard a couple people say they do that a little longer to start cold than what they like, but who doesn't have that trouble with a stock engine?