To save you some trouble:
The EDM/JDM forks that come with the factory clip-ons have longer stanchion tubes than the handlebar clamp models. How can you tell? They're the same forks but the oil height changes in the manual.
If you lower the triples to install the factory clip ons, you either need to drill and tap your existing triple (the bosses are there but are untapped) or obtain the correct triple already drilled and tapped for the clip ons. I would suggest using a drill press for the job unless you are that accurate doing it with a hand drill.
Katana clip ons will not bolt onto either triple without drilling and tapping either triple. The material is there but it's your ass, so caveat emptor. You will also have to factor in the one inch (25.4mm+) drop that will take away clearance from the front wheel/entire bike and alter geometry on the bike to ensure proper overlap on either clip on.
It will get much worse under braking, steepening the head angle under dive possibly causing headshake. The factory damper rods suck and this will really make the situation worse.
If you really want clip ons, I would suggest to get ones that have a rise in the clamp and place them underneath the top triple. This will also necessitate modifying the headlight bracket. Another option with the OEM handlebar clamp are a set of clubmans or Suburban Machinery bars. Barring a complete fork swap, these are the easiest, safest, least expensive options.
If you are hell-bent on running the EDM/JDM setup, I'm sure you can obtain the katana fork tubes and hybrid the forks to accomodate. By the time you've gone down this road, you could have purchased a fork swap already.
If you need a set of OEM clip-ons and the factory clip on triple, let me know. I've had a set languishing in the basement for eons now that I'll let go of.
Good luck.
-Randy