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Seems like it may be pointing towards the transmission input shaft bearing, because if it's unrelated to clutch operation, then that crosses the clutch release bearing off the list.
But it's hard for me to say without being in person lol.
I had a 97 CX with the same problem as well, with a funny bearing/grinding noise in 1st and 2nd mostly heard at acceleration, then was normal the rest of the time.
The input shaft bearing is more or less a common issue with the EKs at this point and basically your two choices are to swap the whole transmission or to overhaul and change the input shaft bearing. At that time, i was lucky to find a cheap transmission lol
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