Do your forks feel like this?

I just had my suspension done by Jeff including Gold valves in the forks, however, I'm running Eibach 43kg XR400 springs at 5mm of preload. I don't have any glitches. It's nice and smooth even with the new seals.
I would check your preload spacers to make sure you have the usual 5 to 10mm of preload, not having less than zero preload and having some slop in there. I've also heard that rotating your springs a little in the fork tubes can effect clicking sounds.

It sounds as if something is not quite straight. If the springs are sort of bent, or at a slight angle - you will get that notchy feeling you describe.

Also make sure your oil is exactly the same in both legs.
sn

Loosen the bolts on the lower triple clamp, then upper triple clamp (bike on stand of course). Hold the front wheel between your knees and twist the bars back and forth. Center everything up and tighten the upper clamps first, then the lower. Sounds like fork bind. If not that, then take the front wheel off and see if the problem is just with one fork or both. Probably only with one fork. Remove the cap and pump the fork to bleed any air that might be in there.
P.S. I'm not saying Jeff forgot, but make sure you have fork oil and that it is at the right level. It's been known to happen that it gets left out.

what you may be hearing is the "slop" in the floating front brake rotor being "taken up" before the forks compress.

what weight and brand of fork oil are you using ?