Flipping C1 and C2 (from instructions) changes front roll center and in affect gives you much more aggressive steering. After flipping it, you will need to change your setup to tone it down
Downtravel, drop, rebound stroke...there are many ways to measure it. You can:
1) Use setup wheels, measure the ride height, and then lift from the center of each end until the setup wheels lift, measure that and the difference would be downtravel. That's how some setups call for 2mm or 3mm etc...
2) Take off the wheels and place chassis on the setup board, use calipers and measure from the top of the axles to the board. A lot of drivers do this, that's why sometimes you'll see measurements like 24.5mm or 25mm every now and then.
3) Take off the wheels and place chassis on the setup board and using a ride height gauge, measure the lowest point on the suspension. Try to find a reference point and always measure from there. Typically this would be the hub for the rear suspsension. On the front, draw an imaginary line vertically from the outer hinge pin and measure from there. After setting, ride height, camber, etc. put some setup wheels on and adjust spring preload to take out tweak. Some setups using this measurement will have something like 5mm, 6.5mm, 7mm etc.
It would help if the authors of the seutp sheet would note how they measured this.
I hope this helps.