-12 , sounds like some kind of usb fault... probably device not ready, you shouldn't be getting this, sounds like some kind of (PC) hardware issue.. cable,hub, etc ... check you have power saving off on the usb.
anyway, not related to you compile issues, and looks like it 'finally connects', but perhaps when can compile it may or may not give issues...
debug - no real debug mode, but if you start Axoloti from the command line, you will see a whole load of more messages displayed
scripts, are in the app/firmware folder ... if you check them, you will see what environment vars they need , these are setup within the application.... I think though, they generally default correctly.
(I don't really use them on windows, or from a runtime image, but they are the same as the dev ones)
as you will see, the scripts really just set things up, at the core (unsurprisingly ) we use Make to do the compilation.
Id also suggest you try to download and reinstall the axoloti_runtime, as this is the part that seems to be giving you problems.
(fyi, ive got a windows 10 laptop here, latest updates, 64 bit and its running absolutely fine)