Thanks for the ideas. I'll pull the pan next week and see if the filter extension might be sucking air. I forgot to mention that I have a deep pan on it with one of the earlier stamped filter extensions, and I recently read that they would many times not seal properly to the valvebody, causing cavitation. As for the clunking, I only notice it when taking off slowly (drivetrain not under tension) so I guess its something I'll just live with. A few nights ago I was under the car and noticed that I have a huge amount of side-to-side play at the trans tailshaft yoke, so I'm also thinking that this may be what is causing some vibrations I also feel at cruising speeds. It looks like its time to pull the trans and rebuild it, as there is a slow leak from the input shaft seal and fluid drains from the converter overnight. While I have it apart, I'll replace the tailshaft bushing as well. This will be my winter project this year...
Thanks,
Mark