I am the author of the mod on github. The design of the two-knob system on Bravo running with the standard in-SIM default control drivers does easily control all KAP140 inputs as you say. What a lot of people do is run a third-party control mapper like AAO, spad.next or fsuip. You could then map the unneeded buttons VS and IAS to UP and DOWN directly (H:KAP140_Push_UP and H:KAP140_Push_DN). Or any other buttons on the equipment you have. Or even two keyboard keys. The readme for the mod has some hints on this. You will want to think about 1000s and 100s on the altitude setting too.
Of course going with the 3rd party mapper has expense in both money to purchase and time to learn how to configure.
The goal of the KAP140 mod is to correct incorrect status display on the KAP140 screen. Generating the correct external control inputs, i.e. UP and DOWN, is really another subject.
If this is all too big as mess for you, can always use the mouse to hit UP and DN. The first press shows current VS, and additional press will inc or dec.