These are the breather tubes for the transfer case and the transmission, they are supposed to be mounted above the front of the bell housing of the transmission in the same area that the front differential breather tube is positioned. They are mounted high so that water doesn't go into the tube (especially when fording water).
Maybe during engine work, someone unbolted the mount (in the engine bay) and left it unbolted; over time, it worked its way down the side of the transmission. It will be difficult to work it back up to where it belongs. Find where it is supposed to mount, make sure you have a bolt, have someone with a rope from above pull it up and someone helping guide it from below. It's a very tight fit.
If you're up to the work, you can remove the transmission (adapter/extension housing) mount to give you some room above the transmission. Be very careful to support the transmission with a jack though.