To Clunk or Not to Clunk.....
I've got a similar problem with my 96 X. Sometimes it'll "clunk" when engaging and sometimes it shifts smoothly.
I had never been one to wait for the full stop before shifting into reverse (from a forward gear) or out of reverse into a drive gear, but after i had the tranny rebuilt in April i've made sure to come to a complete stop as a precaution. I've noticed that neither waiting for a complete stop nor rolling forward (or neutral) has made a difference as to how the shift into reverse feels/sounds.
Prior to the rebuild, i was told that i need 2 (out of 3) new u-joints in the rear (split) driveshaft. I would assume (seems probable) that loose u-joints could be the culprit, but i have yet to address my issue. I'm guessing that the reason for the clunk/no-clunk depends on where the d/s comes to a complete rotational stop before the shift into reverse.
So, i guess after all this, i'm in the same boat as you.