After countless hours of work, I've finally completed my AR3.5 robot build (AR3 upgraded to use the Teensy 4.1 from the AR4)!
As per the AR3 --> AR4 upgrade sheet, the limit switches need to be wired to the 3.3v pin on the teensy rather than the common VIN pin that the encoders are wired to. The way I did this was to use a 4-pin aviation connector rather than a 2-pin one and used one of the extra 2 pins to wire the positive end of the limit switches to the 3.3V pin. If anyone wants to go down this route, just keep in mind that the cables on the corresponding 4-pin aviation connector in the control box would need to be wired in a mirrored fashion (see picture attached). The white cable in the picture is the encoder cable wired to the 3.3V pin - the wiring in the robot itself is an exact mirror image of this (horizontally). This would allow us to use an identical 4-pin cable as the ones we have used to connect the motors to the control box (one less thing to keep track of).
I've also managed to get the AR4 software to run on macOS. Turns out that the prefix "COM" was hardcoded into the code which would not allow us to enter the port name in the mac format (which in my case was /dev/cu.usbmoden1452). I also managed to fix many of the layout issues that occur when running the software on a mac. I've attached the updated python file for anyone to use.
If anyone needs help in building the robot, check out the YouTube series by Chris Boden (under his channels: Chris Boden and Chaotic Good - the robot playlist is called ARchi3). Although the series is not yet complete, it goes through the bulk of the build.
Special thanks to Chris Annin for creating this amazing robot and putting it out for us to use free of cost! Looking forward to anything and everything you have in store for us!