Your images show the shift linkage is clearly way off.
It needs to be at 90 degrees, the shifter arm that goes on the tranny.
Loosen it up and line up the dash and the dot again.
Adjust location of shift rod at other end. Use these images.
You have your rod connected to the GP shift position not standard shift.
Edit to clarify: On the rearsets, not the shift arm at the bike.
Rotate and align the marks. While its off move the other end from the GP shift position, then reattach to the tranny.
If you move it to the back mount hole it will take some of the length out of the shift rod and put you where you need to be.
Insufficient information, pictures not detailed enough or clear enough. Need better lighting highlighting the brake attachment to the rearsets. Looks like something is way out of adjust driving your pedal very low. Also there is no sign of your rear brake switch. Lets us know whats going on there and how you want it to be when your done and we can get that squared away. Take some straight on photos with flash of the brake side.
Off Topic, sent you and invite to California Facebook group so you can find some local rides.