if you found nothing between the engine and hyd pump area wrong i would pull the cover off the top of the flywheel housing and check the flex plate on the torque converter and make sure it is ok, may have a broken flex plate. (this is common on these units but is usually accompanied by a noise when running coming from the flex plate rattling)

if nothing is wrong there it might of been a cylinder not firing correctly and engine missing causing the vibration, then something let the cylinder start firing and that might of been the clunk you heard, maybe a small backfire or something... when all cylinders started firing again, it smoothed out.
Bad wires can cause this.