Sheddah ... I can relate to the cabinet issue! I got a new cabinet last year locally made, but probably Horn-like. For mine the shelf that the machine sits on in order for it to be flush with the table top brings it down lower than I really like. And too, I can't really get that 90° on the knee and ankle. I did a lot of FMQing on the weekend, and at times my foot/ankle got too far in front and oh my how my ankle got overextended and uncomfortable pretty quickly. I had to stop a few times and re work the positioning. It would all be OK if the foot pedal were not so high by its own design!
It looks like you are on track for figuring it all out ... just keep at it and you will. One thought I have had and might work for you ... is to put the desk on top of blocks of wood, in order to raise it up a couple of inches. Haven't done it yet, as would take some help and I want to make sure it would be a highly probable solution! Raising it, then affects the chair height, so would I gain? or would it just change all the other heights and angles and I would be no further ahead?