The bottom part is the shock body. It is best to do your primary height adjustment by adjusting the shock body. (Caution: Don't make your shock body too long and lower the spring perch height... you can easily reduce your suspension travel while having what appears to be adequate ride height! Sit and ponder that while looking at your suspension until it makes sense. )

The upper adjustment is the spring perch height. It adjusts "spring preload". You want to adjust it up high enough that your springs have some tension on them and don't fall out of the perches under full droop. You can do minor height adjustment with preload, as well... but see the caution above. I usually like to set the shock height as short as possible and use preload to set the ride height. That way, you've got maximum suspension travel. Of course, there are instances when you wouldn't want to do that, and possible benefits to doing it other ways (like if you were running softer springs and using the bump stops as a "progressive rubber spring", like the stock Miata suspension does).

Rear swaybar is good, and I know the Hondas are known for breaking swaybar mounts with big bars, so the brace is a good idea, too.

To answer your last question: NO, you can't adjust spring rate. It is what it is. Only way to change it is to get another spring.

But, with your giant rear swaybar, I'd try what you have and see how it works. Odds are that you'll find the ride to be stupid stiff, and it will probably understeer just a little bit. Ultimately, you'll likely decide to fix both of those issues, and the way to do it would be to go down in front spring rate. Somewhere between 10 and 12kg would probably work well with your 9kg rears. Alternately, if you find the ride COMPLETELY too stiff, you could see if the 9k's will fit the front, and get something like 6 or 7kg for the rear.