M belt pulley gearbox

I am trying to remove the belt pully gearbox from my M to get into the transmission. There are threads sticking up through the gearbox cover, large probally 3/4" one on either side. Are these used to secure the belt pulley gearbox down to the transmission cover? Do I need to pull the whole transmission cover to get the top of the gearbox off? I took out the 4 - 1/2" bolts in the cover and the gearbox won't move.

I know picture would be worth a thousand words but don't have one right now.

I downloaded the M&W 9 speed manual from Neb Cowman's site and the pictures don't match what I have. His shows a cable to operate the shifter inside the tranny but mine has mechanical linkage that doesn't mesh (pin in a slot) I have to get the broken off plug out of the bottom to drain the oil out to see better but did M&W make a change to their 9 speed shifters at some point? I thought it was behlen that had the cable operated 9 speed. Mine has M&W gear cast into the actuator lever on the outside of the tranny.

Maybe I am missing something like my actuator cable is laying in the bottom of the gear oil.