Adobe has FINALLY released a 64 bit PDF iFilter. For everyone out there running 64 bit MOSS, without a proper 64 bit PDF iFilter, please go get this for yourself. I haven't seen any performance data, but it should increase your indexing performance of PDFs. Details are here. Instructions for installing on MOSS can be found on the linked page.
UPDATE: Some internal testing was done with this Adobe iFilter. The performance still leaves something to be desired. In a head to head comparison, the FoxIT iFilter still runs signicantly faster. The iFilter Blog has some data on this, which can be found here. It's likely that Adobe is continuing to use the 32 bit iFilter and the wrapper from the previous work around.
I have a program which uses IFilters to do indexing. I got around this by compiling my code in both x64 (main) and x86 (secondary) mode, then putting the appropriate E_FAIL checks into my main code, which then spawned off a console application which held the secondary, x86 version. This makes my life so much easier. Thank you, thank you, thank you.