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I bought my 97 CX (also 16y7) with a bad transmission and installed a J5F VX trans to replace it. Trans ISB was bad so I just swapped it for a VX trans I picked up of Craigslist for $150. While I had it appart, I put in a new autozone clutch kit (clutch, pressure plate, pilot and throwout bearing). No issues at all after the swap.
I would have guessed it to be an internal issue, but with two transmissons doing the same problem? that normally points to something else. Is it possible you damaged a bearing in the swap?
Hope you figure it out as that transmission is awesome!
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