You should have a letter from your PD at minimum stating you were in good standing and what rotations you did complete (along with evaluations of whether you were doing well, satisfactory, or unsatisfactory). Most programs will want to see that.
In addition, you will need to convince PDs that your medical problems (whatever they are) have improved and will not cause you to voluntary resign in 6 months from their program. Consider this for your personal statement.
In regards to your funding, I would assume the worst case scenario and plan for only having 2 years of it (out of the initial 3) for when you interview. I would be upfront about this at your interviews. Probably unnecessary to mention directly in your application (obviously PDs will know given your residency history).