There is a vacuum activated valve for the coolant to cool down the tip. That valve can go bad... mine was seized shut causing some of the gears to slip when car & tip were hot (mostly 4th to 5th). No jerky upshift... just slipping a tad but like yours I had occasional clunking sounds when downshifting tho :/
Changing that tip vacuum coolant valve thingy fixed it, apparently, never had it again. Whatever that valve is called, your indy should know what to look for (really forgot the name for that thing). Cheap, $45 or something.....
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'97 Boxster base model 2.5L, Guards Red/Tan leather, with a new but old Alpine am/fm radio.
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