If I was in your shoes, the first thing I would do is, instead of building/flashing the *converter* firmware, try with the *onekey* firmware
https://github.com/tmk/tmk_keyboard/tre ... ard/onekey
You will still need to adjust the Makefile for your board.
If you're able to flash that firmware and send the 'a' key by shorting pins as described, then you're on the right track -- your compiler tools and board are working right.
Next, I would try flashing the converter firmware without making any changes to the keymap/other customizations.
First, take a totally fresh copy of the tmk firmware without *any* of your changes at all (not sure if you're using git or if you downloaded a zip from github, but either way extract/clone to a fresh directory).
Edit the file Makefile.unimap.alps.rev1 in the ibm4704 folder and change the MCU to at90usb1286. Build the firmware using this makefile and flash it.
If this works, the hard part is done and you have a working board, and you can work on customizing the keymap at your leisure.