As a former ROTC guy and current active duty F-16 pilot some things I'd recommend:
1. Don't stress the fact that you're out of shape now, but start doing something about it nonetheless. If it's something you really want to do, the motivation to get in shape should come naturally. Also, making the minimum cut isn't especially difficult; I've seen some pretty out of shape people wearing the uniform in my time. Of course with your goals you should be getting closer to the max than the min though, but it sounds like you have some time to get there. Also, don't be scared of the G's even if you get in shape but don't significantly "bulk up." I can attest from personal experience that tall skinny guys are out there flying the Viper as we speak. The most important thing is proper G-strain technique, and the new G-suits we wear are a significant improvement over the older ones worn just a few years ago.
2. Getting a PhD while an active duty pilot is going to be extremely difficult. The time commitment of being a pilot in an Air Force fighter squadron is tough to overstate, without even taking frequent TDYs and deployments into account. However, the Air Force does offer generous opportunities for you to attend grad school full time prior to attending UPT. Recommend talking to an ROTC recruiter for details. Whatever they tell you though, in today's manning state do not expect to be released from a fighter billet to pursue higher education later (Olmstead, etc.) unless you are a total rock star.
3. The commitment required by ROTC is minimal initially. Depending on scholarship status you'll be able to walk away no questions asked for the first year or two if you find that it's not for you. At some point you will have to sign on the dotted line though, but you will have ample time to think things over first.
If getting a PhD is really the most important thing to you then I'd do as others have said and pursue the Guard or Reserve (Heck, I'd probably recommend that even if you DGAF about a PhD) so that you have time to pursue your studies.
Good Luck!