What's the linker cable?
It sounds like you've gotten the problem fixed, which is good. The only complaint I've heard of the 6th gen auto trannies is knocking when it shifts, I believe due to the locking torque converter. It's not really a problem, it's just different than how some other autos feel. I've got an '01, but a manual. I can ask a guy at work tomorrow if he's noticed any similar issues with his. I think he's got a '99 or '00 auto.
Honda transmissions usually last a while. It sounds like you've put a lot of miles on your car in a short time, but that's not normally an issue with Hondas until the 200k mark.
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