Is this a pretty universal diagnosis for this clunk? I have the same thing as OP when slowing to a stop from 2nd to 1st. Confirmed that it is drivetrain related because it doesn't happen in neutral.I think what made the difference, fixing the clunk, was adjusting the throttle cable to the trans. It was at about 1mm of spacing, and I changed it to almost 2mm, and now it's much better, and that clunking I was talking about, just before I was about to stop, is basically gone. I think the clunk WAS INDEED timed with the trans downshifting from 2nd to 1st, and it was a bit harder than it should have been. But keep in mind, it was never that bad anyway. There appears to have been 2 problems happening at about the same time.
Thinking about getting into the throttle adjustment this weekend.
edit: well I'm an idiot and thought (per the FSM) I needed to drop the transmission oil pan to get to the throttle cable adjustment. But this one is up on the engine by the accelerator and cruise controls cables. 3 minute adjustment fixed it. No clunk. 80-series Throttle Adjustment - Land Cruiser Tech from IH8MUD.com - https://www.ih8mud.com/tech/80throttle.php
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