You don't HAVE to take the forks out of the bike. It's much easier to do it that way, though. It's a bit of a hassle dealing with spring compression to install the spacer, put in oil to the desired level and such with the forks in the bike.
The time you save NOT taking the forks off will probably be more than used messing with the inconvenience with them ON the bike.
re: preload
The oem preload is ridiculous (too much). Using the oem spacers on a longer spring will only make it worse. Your choice..but there isn't a whole lot of point to putting in new springs if you aren't going to do the job right...imo.
re: fork cap off.
A correctly sized socket would be nice. No, I don't have one, either. I use (sorry) an adjustable wrench. Remember to loosen the cap before you loosen the bottom clamp (if you're taking the forks out. This has been covered before).
re: clicker all the way in
That's unlikely a good thing. It won't be balanced with the rebound, most likely. With a too-hard compression setting, the bike will kick your arse (instead of compressing) on sharp edged stuff. That will lead to a control (failure to keep it) issue. There are a number of other problems with it set that way, too.
Basically, compression needs to be SOFT enough (clicks out) to absorb impacts without jacking your arse, HARD enough (clicks in) to take as large an impact as you're going to give it. Rebound needs to be FAST enough (clicks out) to be ready for the next impact (not 'pack'), SLOW enough (clicks in) to keep the wheel on the ground during the rebound process.
I think you've read that before, too.
re: rubber thingys
A mechanics scribe works well. So will a small screwdriver.