There shouldn't be anything inherently incompatible with x64 in EqEmu terms, but you may well need to ensure you have 64 bit dependencies (perl, dunno if DBI comes in different flavours?).
Over the past 6 months the database has gone through masses of changes, and development seems to have stepped up a notch with LOTS of changes too. I recognise some of those errors from other threads (merchants/buffs) so it might be worth looking through both the Linux and Windows servers support threads, or post a new thread for each one, which might attract a bit more attention from the devs or someone who has already had that issue