You may be able to observe what leads up to the clunky shifts. For example, if you're going 50 mph and coasting to a stop sign, and you try to get back into first gear while you're still going 35, you're going to hear quite a clunk as the dogs engage and force the gears to suddenly make a big change in speed. In this example, waiting until you're down to 10 or 15 mph will allow you to get into first without the clunking.
See if you can tell what events lead up to the clunky shifts and let us know.
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