I'll try to answer your questions as best as I can.

When I connect my N800/OS2008 to my Vista PC, I see both memory cards as separate drives. I believe that is the normal behaviour. Is the next drive letter above the card you see available on your PC? Wondering if you have a mapped network drive or something at the next logical drive letter.

Doesn't sound easy to put apps on the cards. See my similar question and the answers here:
http://www.internettablettalk.com/fo...ad.php?t=12274

No speed difference between the slots that I've heard of.

Mixing OS2008 and OS2007 in dual boot results in Wi-Fi not working.. can't remember which is broke but I think it is OS2007. There are other threads that discuss this... sounds like you found them.