I'm looking into buying a 2009 Series 2 RX-8 R3 with a brand new engine and trans (less than 2k miles on them) and 102k miles on the body and am wondering how reliable it'll be. I'll be driving it to and from college which is about 610 miles one way twice a year and don't want it to really have any issues while going to and from school.

 

Get a different car if you want a car that can handle long distance driving. Would recommend Honda or Toyota if you need something dependable.

 

Eh, I always enjoyed long distance trips in my 8. But, the R3 Recaro's may be less comfortable when you're in them for hours and you're going to burn a lot of gas. Perhaps not ideal for college budget.
Reliability-wise, IF the engine is new and everything was well maintained, I wouldn't expect any problems.
That's not to say there won't be problems, just that there won't be more problems than any other car at 100k miles.