!st off, it's not a sports car and not designed for speed shifting
take your time shifting and it will be a lot happier.
the clunk is a sign of something having excess clearance or being loose, crawl underneath the bus and make sure that all the bolts on the driveline are tight, bellhousing to engine, trans to bellhousing, u-joint to trans flange also the nut that holds the flange onto the trans, carrier bearing to frame and the rubber bearing mounts, check the rear end for excessive clearance or gear lash. then start looking at the rear suspension, are the axle to spring u-bolts tight, what condition are the spring mount bushings in etc. if you don't find an external reason for the clunk then possably their is something internal in the transmission that is not clearanced properly.like the end play on one of the shafts, or a failed snapring retainer.