The spec on a 5/8" shaft collar is pretty consistent. I checked your link before you ordered and it was the correct thickness. The OD is 1-1/8" which is what you want.
The 550 stops are underneath the triple clamp, so it's not easy working under there, and the clamp stops are not round pegs, they are sorta like curved fingers. It would be tough to drill and tap a removable appendage there. You could maybe drill through the main frame peg/stop to make a removable stop.
Just got the shaft collars in the mail, put it on and put it all the way to lock and it looks like my clip-ons will still be able to be at the angle I want with minimal compromise.
I'll put them on this weekend and update with pics.
Also, I have found some short Z1 clutch/ throttle cables in the japanese market. Your custom cables run 1184.3mm - 1190.6mm. These short cables say they run 10cm shorter than stock. so from the stock z1 cable (i think its 1282.7mm) will put the short z1 cable at 1182.7mm!
do you think the 1.6mm difference wouldnt fit well when my clip-ons have a raise to them? might have to lower them..., till then I can just run the looped stock cables.