Sorry to hear about the accident and the not passing...like others have said, RTI will allow for one free retest once you are healed and back up to it, both physically and mentally.
As for where to go from here, I'm assuming you don't already own a bike? If that's the case, I'd talk to RTI as I know they also will do private lessons. Sure, it will cost some extra money, but it would be golden 1-on-1 time with an instructor to help you get past any hurdles you might have now.
As for some of the other points you mentioned...I also did my M2 with RTI having never rode a motorcycle before (I owned a brand new CBR250RA I had just bought, but was too afraid to throw my leg over and potentially drop it having 0 experience). Although RTI won't readily admit to it, some of their bikes are a little dodgy from being dropped and repaired...or just from general abuse. I found none of the bikes I rode behaved exactly the same, and all had quirks about them. When I did ride my own bike for the first time, it was like driving a Cadillac in comparison. At least in my group, everyone sort of claimed a bike on Day 2...so I made sure I got one that worked well enough for me, and made sure I was first back to that bike the remainder of the day.
As for shifting and rear brake -- I can see the process of shifting being hard for some, especially if you have no prior experience to it. I think I was ahead of the game as I learned to drive stick at 16, and have only owned manual transmission cars since, so I just had to get the physical differences down vs the thought process. Clutch engagement point also can vary depending on wear and cable adjustment, so the bike you had might have been dodgy on day one...I know one of the ones I rode was that way as well. For rear brake, the reason is to keep the chain tight and it actually does help with low speed stability. Also because if you use the front brake at low speeds with the bars turned, you'll end up sideways rather quickly.