There are regular clunks that do occur occassionally on the VX that are not major issues. Low fluid can cause some shift issues but if it is a big hard shift (can really hear and feel it) going from 1-2 or 2-1 then it is probably the Mode Selector, a $300+ part. If you have a 100K warranty on a '99, take it in. Aftermarket parts you mention are not the cause nor should they be an issue with warranty. But I think it is the standard clunk when coming to a stop.
Also do a search on here for clunk and you will find a better description of the known issue.