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I recently bought a 2001 Gt the owner had already put a bunch of parts in it and he e planned what the sound might be but in not totally sure. He installed a short throw shifter and now when I'm idle or at low speeds there's a little bit of a rattle sound he said it's just the shifter, although I think it might be the gearbox. Has anyone had this problem before
check to see if the shifter seal is seated properly, (the one that seals the interior from the outside) the tr3650 is pretty noisy and not sealing out the sounds from it could cause your issues.
In addition to the above post, just be aware that any aftermarket shifter will transfer more noise than the stock shifter would. Based on your description I see nothing to be alarmed about.