Okay I followed all your suggestions most of which I was following from your video tutorial before. I was seeing no errors in the console. When starting the game I am pretty sure its trying to have my stick take player 1 spot; as sometimes LMTK was working as expected and other times it was not.
I have noticed if I wait to plug in my stick until after I have started the game up it does seem to use LMTK as the player 1 as expected. So that's what I have been doing now.
There is one other odd behavior I have noticed, for some reason the game reads my A/B and X/Y inputs swapped (eg A is B, X is Y, etc.) I have fixed this on my side by just creating a custom controller layout in steam for the LMTK controller to swap them so it reads correctly. Really not sure why that is happening I've observed this issue on both Xrd and +R but have yet to try any other games yet.
Also as a heads up when using configure midi and trying to save config it pops up to open instead of save. Grabbed a screenshot of it to show you (note Save config is grayed cuz its been clicked)