Just as Jay said. I'm at .250" from the top of the cap to the t-t. Torque the top bolts to 14 ft.lb and the bottom to 22 ft.lb If you broke them loose, just spin the shock by hand pushing up, it will go easy. Make sure you can lift the front end to remove some pressure. If not the shock will end up bottoming on the handlebar...Marthy ,any chance of pics of your mod .Maybe a pointer or two as to where to measure from.
Thanks in advance.
Edit::
I can see you mention from top of the cap to the triple three so maybe a pic of that .
Cheers
I used my Red neck stand and lift the front wheel using a floor jack under the headers... work just fine.