I'll try to answer some of your questions until Pima can weigh-in with more knowledgable information.
If I understand this right... you go before a board to get into ROTC (AFROTC) initially...
No. If you are applying for a HSSP (while in high school) scholarship you are evaluated by the AFROTC scholarship selection board and a determination is made whether to award you an HSSP Scholarship. If you do not receive a scholarship then you can still join AFROTC (without being reviewed by a "board") simply by contacting the AFROTC Detachment at the college you will be attending. There is some paperwork....but nothing too major.
...once selected, before your Jr year, you go before a board again to see if you are selected for SFT (based on grades, leadership, work ethic, etc)
This review for SFT actually occurs after the 1st semester of the sophomore (200) year (Jan/Feb). Supposedly both scholarship and non-scholarship cadets stand an equal opportunity of being selected. Although you did mention grades, leadership, work ethic, etc....your college major (technical vs non-technical) is hugely important and commanders recommendation is a substantial portion of the evaluation.
...if you don't get selected you may go before board again as a rising senior.
Yes. After your first semester of your junior year (again Jan/Feb). At this point you are considered a "250" cadet and are actually behind where you need to be in the AFROTC program. The chances of being selected for SFT as a 250 are not good and if selected you may need an extra year of college to "catch up' with your AFROTC classes. It is generally at this point (before the end of sophomore year) when cadets that are not chosen for SFT will consider changing branches or leaving ROTC all together. Of course some will come back as 250 cadets and take another shot at getting SFT. Another year of college may not be too bad if you are using it to tackle one year of your Masters degree.
SFT is a must to commission, but grades, SFT, class rank, etc are what determines your odds of getting one of the career choices you select??
Yes. After you successfully complete SFT you will compete nationally for your AFSC.
Also, when you mentioned transferring branches...how common is this?
Not very? Depends on the person. If they are determined to serve in the military and they are willing to serve in a branch other than the AF, then they can apply to a different program.
I would think you would have to put in for a different scholarship with the new branch?
If you had an AFROTC scholarship and changed branches, your AFROTC scholarship would end. You could apply for a scholarship from whichever branch you transfered, but the in-college scholarships for all branches are getting rarer. Of course you can apply to (and join) another branch's ROTC program without a scholarship.
Is there a chance the SMC/school wouldn't want you then?
If your academic CGPA is above a 2.0 then most colleges won't care whether you are in ROTC or not. However, if you are asking whether other ROTC programs will want you or not....that will depend on where you are in college (which semmester) your major, CGPA and how well you can convince them that their branch was what you really wanted all along.
I should mention that my answers to your questions may not be completely accurate in regards to SMCs. They all have different policies and you would need to evaluate each individually.
Good luck and don't hesitate to ask questions. Some how we all had to learn the same things you want to know. Every question you ask (and that gets answered) is probably helping some candidate/applicant and their parents.