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Hi TJ,
That upgrade path is fine, and quite common; as long as the shared storage is the same (I assume it's already a UNC path), then when you start everything up again (webserver, indexing service), it should be the same.
There isn't so much risk going from 3.5 -> 4.0, but please do read the ProGet upgrade notes just to see what's coming.
Just make sure to do a quick test on the current (2005/single server) set up as 4.0 before moving that to new servers. You can always rollback if there is a realy big issue (though, we haven't seen any yet!)
Best,
Alana