Poop I stopped reading at page four.
You need a brand spanking new transmission from Honda. Not a refurbed, not a used, etc. You have a 5 year 60,000 mile powertrain warranty. The transmission was ruined by the mistakes of one of their techs. In no way shape or form is this your fault or responsibility. This dealership needs to suck it up and replace it under warranty as it should be. Keep pestering Honda NA and the Service Manager. The Service Manager is giving you a load of crap with the 20k mile one, he's trying to save his dealer the paperwork and money involved with the warranty work. Much easier for him to find a used one, foot the bill, pay his tech and be done with it.
Sucks you have to go through with this but E36 M3 this is your car and fight for your E36 M3.
I went through the same nonsense with Subaru. Copper chunks in the oil, three dealers later none of them would touch it with a 100ft pole and all told me that "When she blows we'll replace it no problem." Subaru North America stood behind their dealers and stated the same. At least the bullE36 M3 flowed consistently. I got something out of them which helped for a new Honda Civic Si, but I got somewhere with enough pestering.