Wrong.
I could put a set of Vortec heads on a 283 from the 60's or put a set of bowties on a on a 1996 block.
Engines with a 2 piece and 1 piece rear main seal are different. Intake manifold has nothing to do with what the short block is, just what heads are being used...
Your engine is most likley a 1 piece rear main seal small block. Post your serial number for 100% certainty. Try tracking down the source of the water intrusion before jumping to conclusions. There is still a very slight chance it may be something stupid that allowed the water in.
If you are looking for a good deal on a long block check out Rapido Marine. I bought one of their engines and had it sitting at my front door in less than a week...
http://www.rapidomarine.com/default.aspx?p=/engines/default.aspx