1. The main thing to do after you flash is to make sure you hard reset the device (hold down the 2 soft keys (that look like a dash) then press and hold the soft reset button in via stylus). You should be prompted with a dialog asking if you really want to clear your storage or not. If you don't see that prompt then you haven't hard-reset.
2. The only thing I can think of as far as skipping on music playing is if the music is encoded with a really high bit-rate and/or the storage card read speed is just absolutely terrible.
3. I have the DLink DSM-G600 wireless/wired NAS that has treated me pretty well with a 500 gb HD. (
http://www.dlink.com/products/?pid=377) You can find it new for ~$100 (minus hard drive). Just make sure you are buying a rev B version, I heard bad things about the rev A versions. I use it as my 6700's wifi point at home and I have no problem browsing the contents of the G600 with Resco File Explorer.
Edit: So to get this to work in your car you'd need to find a regulated 12 or 5 volt power supply (forget which the unit needs).