Good work
The PCB looks to be single sided so if there is no trace going to a pin it goes nowhere and is available to use for your trackpoint or OLED.
There are two pins on the JST that have black wires, those would be ground and shield ground and they go to the bottom two pins in both the red circles as you said. The other side (blue on the JST) is 5v and that goes to the pin above the two grounds on the left.
The USB data pins don't have as much current so are much thinner, these go to the top two of the right red circle set. In a standard USB cable D- is white and next to 5v while D+ is green and next to ground and that matches your JST so that's probably accurate. If not it just wont work and you would need to swap them, no harm done. It's only if you plug the 5v into a data pin that you release the magic smoke.
I'm not sure where the top pin of the left set goes - maybe it loops under the JST socket to be yet another ground? Just ignore it, you have somewhere to connect all four of the wires needed to get the USB to the Teensy.