I was just thinking there maybe a 'bump stop' in one of the legs, I can't remember if there was when I had mine apart, and if you had one leg slightly lower than the other in the clamps, the leg without the bump stop may top out first and make that metallic clunk. The manual tells you to measure from the top of the leg, not the cap, down to the bottom yolk, most bikes you measure from the top of the cap to the top yolk, on the Skyhook forks the caps are different thicknesses hence if you measured that way, as I think I did, your forks would be slightly different heights. Just thinking aloud here, I'll check mine over the weekend.
Good point, I'm certain it's not topping out though I do have a very slight difference of height (maybe 1mm at most) at the moment looking at the fork tube tops. Need to sort that. Also going to look at my steering damper as when I put it all back together the steering seemed a lot lighter than with the old Tourance Next tyres on. I've switched to Dunlop Raid tyres so it will feel different. New tyres always feel very different anyway ...
