Just found this and wanted to say it looks really cool. Hope you are holding up ok.
Not sure if this is still an issue, but about the HMs, I have two possibilities to add to the list.
1. using the HM as a modifier, ex. using cut to modify X-scissor so that x-scissor could be used as cut would be
2. having a stronger version of the HM available, an SHM if you will, that you could get later in the game compleating a type related quest for the gym leader
again, thanks so much for doing this, and I hope you are doing well