Congratulations, you found the PTO! The piston thingy is the shift rail, just attach a pushpull cable to it if you want to use it.
If it bugs you too much I'll trade you the PTO for a blank cover.
It runs off one of the idler gears in the transmission and it used for powering pumps and winches on trucks. They are rare on smaller trucks but they bolt to any SM420 transmission.
