3 things come to mind:
1. Put the bike on the centerstand, then rock it back so the forks are off the ground, then forward to compress them, several times. If there is rust and crud in a few of the damping holes, this will help dislodge it and flush it out so the lower end of the damper can fill up again.
2. If the oil amount was less than 7 ounces, add some more oil. Many manuals I have seen lately have the wrong oil amount. Add at least 1 ounce of oil to what you have: for example, after a full rebuild where the parts are dry, it takes about 1-2 ounces extra oil to fill things up properly again. Draining the forks via the little drain bolts doesn't really empty everything by itself: you have to remove one fork cap at a time, then pump the open one (and make a mess...), then repeat on the other side, to get it all. Then you have to refill the inner dampers, as described in #1 above, or they will 'clunk' on small bumps until they finally refill by themselves.
3. Make sure the steering head is tight: if the balls and races are still there (i.e., no one replaced them with tapered bearings instead) they may be worn and loose. You might just have happened to notice it now after other work...
