The order of the SATA ports is not supposed to matter, but I think there are still some problems. I think they're being fixed in 8.01. You shouldn't lose your data and you can reinstall FreeNAS on another stick, but don't forget to
1) go to Settings -> Config and save your settings
2) If you happened to make any changes to loader.conf don't forget to back that up too.
To get FreeNAS to recognize your pool again:
1) Go to Storage -> Volumes -> View All Volumes -> Autoimport (which is an icon of disks with a circle of arrows).
Your mileage may vary, I had to go to beta2 to get it to import my pool again. Some people's device names like 'ada0' ended up being some long device ID instead.