I always choose Linux, but I will be the first to admit I'm not completely sure what the difference is between the two.
Yes, you can switch to dedicated but I've never used a dedicated host so I'm assuming they just upgrade you without you having to move any files just as if you were upgrading between shared plans.
But call the Hostgator folks (if that's what you decide to use) just to make sure there aren't any issues. I can't see it being a problem.
Don't worry, you haven't kept me up. I did it to myself... gotta get this new site design done!
That's OK I slept till 10am. LOL