I don't know about the marking, but you can easily pull your t-case off before you remove the trans. that will make it easier to remove the trans and get it out from underneath the jeep. Check jeep forum for the marking issues. Or contact Knucklehead on here or JF.

 

I would pull the transfer case first and then remove the transmission.

I don't know why a service manual would have you mark the flex plate and torque coverter before separating them?

What manual are you using?...

 

Torque converter lines up to the holes just one way. It's easier to align while out then mark for easier installation.

 

well, I pulled it out - and took the transfer case off first. Definitely made it easier. But I still need a lift! :mad3: .....
As for putting the rebuilt trans in, I just set the torque converter in, seated it properly, and lined all the bolt holes up. I spun the converter until it a screw hole matched up and then the rest of the 4 screws went in easily - actually pulled the converter to the driveplate.( I made sure the transmission housing was mated to the engine). I did spin the engine clockwise to put the rest of the bolts in.

Oh - and here is a video of the transmission that I took out - yuck!
32rh transmission - YouTube
Don't know what the previous owner did! But that is why I got it at a great price! I cleaned out the lines and the cooler in the radiator with a few cans of Kooler Kleen

 

Are you sure the trans cooler flowed? Shop claimed mine was clean and when I pulled the rad it was clogged solid!