The constant mesh gear at the very front of the trans counter shaft (botton shaft) and the gear on the input (driving) shaft are under load when the trans is in any gear but 5th. The PTO and the Hydraulic pump (Liftall) are also driven from that gear. If it has a chip, or broken tooth, or a piece of netal imbedded in it it will Knock. It is esaily seen through the Belt pulley mount, W/O removing the trans top. It turns modestly and might just be the issue. I am sure you checked each tooth when transplanting the gears, but a cracked tooth can go un noticed. Best of luck, Jim
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