I'm about to remove the Showa forks on my 2004 749s and have them refurbished. I haven't done this before, but it all looks straightforward. I don't have a front stand that lifts from under the bottom yoke, so I will suspend the front of the bike from my garage rafter with the rear end on a Motrax paddock stand. What I very much would like to do is to replace the clip ons in the same orientation that they are presently in now. When Rob at Pro twins set up my suspension 3 years ago he adjusted the angle of the clip ons. To do this he removed a tiny location pin that held the clip ons in the standard factory default position. I won't have this pin for location anymore so will probably mark their position relative to the top yolk with a felt tip pen. Would appreciate any tips of potential problems that could crop up from anyone who has done this before.
Iv'e removed the showa's on my 999 to replace springs before and cant see where you'd have any probs, I did the same as you and suspended the bike from a rafter.
