I don’t believe that boot time is slowed down by the SD card. A Fuze with V1 firmware can only run V1 firmware. A Fuze with V2 firmware can only run V2 firmware. However, it doesn’t really matter whether you but a V1 or V2, as they both function more or less the same.
The music is where ever you put is (or, should I say where ever your Sync software puts it). I find that music is usually placed like this:
Music(artist)(album)(songs), although this formula might very. Ultimately, the Fuze should play any song, regardless of where it is.
Rockbox without equalization shouldn’t sound any different from Sandisk’s firmware without equalization. It does seem to consume more battery, according to rockbox.org (see here).
The best deals you can get on memory cards will usually come from Amazon.com. Just be sure to buy only new cards, as used cards might have been hacked to say they have more capacity than they do (for example, a two gig card might have been made to look like a 16 gig card so that the seller might sell it for more money than they paid to buy it). Do yourself a favor, don’t fall for this scam.