I finished rebuilding my forks, new springs, oil and modified the dampening rod. I notice now that when i hold the front brake and move the forks up and down while sitting on the bike that there appears to be a notchy feelings, not unlike lose steering head bearings. Note that I replace the steering head beerings and torqued them to the correct value. They are not the problem. How can I determine what the problem ??
I just went out to my garage and checked my stock setup. It does the same thing. Almost like a "klunk" when it is between compression and rebound where there is some sort of slack. Did you notice this before you started? Since mine is doing it as well, maybe it is normal.
One very popular problem is people installing the forks unevenly at the front axle. The one fork is offset accidentaly causing the forks to have a 'notchy' feeling. This may be your problem, or it may not.
To make sure they are straight, put the bike on a stand so that the front wheel is not touching the ground. Then loosen the front axle pinch bolts on the fork. Then spin the wheel and squeeze the front brake so that the wheel suddenly stops. Do this a few times and then tighten the bolts again, this should do the trick.
Newer ('H' model) bikes have a floating front rotor. Holding the front brake whilst doing a bouncy on the bike will result in something similar to what you're describing.
'Stiction', or the hesitance you feel when the pressure requred to get the fork tubes 'unstuck' from the sliders/seals is applied, isn't uncommon.