I don't believe an LS2 valley cover will fit a 3rd gen 6.0 block if I understand you right with what you're proposing. When I swapped my LS2 for LQ4 I got an LS6 valley cover and 3rd gen cam sensor to plug the hole (used the LS2 front cover and cam sensor). The cover had the gaskets in place to seal over the knock sensor bosses in the 3rd gen block's lifter valley.
Bill Winters AKA Farmvette
'05 Corvette - Forged 408 Iron Block + TTIX | 980/970 @ 24# : 1120/1100 (150 shot) | 10.15 @ 150 MPH (a few hundred HP ago)
"When life hands you lemons you upgrade to a C6." - Me