It's a virtual certainty that Asus added support for 45nm processors among the many updates to the BIOS on that ultra-popular board over the four years it supported the board.
Doesn't matter anyway. I did the exact same upgrade path as the OP and I got a Q9650 running on my P5W DH without doing anything beyond BIOS upgrades. Only downside was the CPU overclocking settings were locked...as in completely invisible.
I do believe that later hardware revisions of the board had a modified voltage design, which is probably why they put Yorkfield support in beta. So it's really a crapshoot if it works or not.
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