Man this summarized build thread seems to go a whole heck of a lot faster than the actual build did.

While I had the engine and trans out I cleaned them up with degreaser and a pressure washer(for the trans/transfer case). The engine was in good shape and cleaned up sufficient enough for my purposes. I ended up throwing new plugs, plug wires, oil pan gasket, rear main seal, valve cover gasket, power steering pump, and all new hoses/vacuum lines on it. Both the oil pan gasket(rubber/metal kind) and valve cover gasket would have been a nightmare to reinstall if not for using some RTV to keep them in place while I cinched them up. I also put new seals on the transfer case outputs as well as the "pan gasket" underneath. There was a slight leak from under the Dana 300 before I started the resto. Then filled it back up with ATF and the T-5 back up with the recommended synchromesh oil.
Here is the engine on my trusty Harbor Freight engine stand.
Me putting the engine back in using a rented 1 ton hoist from Sunbelt Rentals, only 70 bucks I think? And we were able to get it in my wifes Honda Civic for transport to/from

Man I need a truck....better finish this rebuild!
Thanks to JimsChopShop and the use of his Tranny Jack my Dad and I were able to mate the engine and trans back together with little to no swearing or throwing things around the garage

My Dad(who gave me the Jeep) has called me crazy for wanting to restore it but is always eager to drive the 4 hrs down to my house to help out.
After the engine/trans were back in I put in the drive shafts along with some new Tom's Woods U-Joints purchased in a group order along with OneTon. If anyone wants to know how to install/uninstall u-joints without a shop vice or a press(the appropriate tools) please let me know.
By this point I couldn't stop imagining myself driving the Scrambler again and what a great feeling it was. In the back of my mind however was the large sums of money that were looming on my FISCAL CLIFF with regards to body work in particular. I get sent on a lot of trips for the Military so I have been stashing my per-diem in a slush fund that the wife has Ok'd.