Love seeing you young guys take pride in historical restorations. there may be a couple of things I might do different but you're actually out there doing it, and I'm in my armchair, so more power to your elbow and I doff my hat to you :)
Nice job getting her back up and running. Sounds like maybe the tappets need to be adjusted, but that's easy to do. Also there are clips you can get to run the rear lamp wiring, the clips go under the bolts on the shifter plate if you want to make it look a bit more original (same for under the hood and behind the dash). Part numbers are 9N 17667, 9N 17668 I believe for the rear lamp clips. There is a 365 page Ford Shop Manual for the 9N, 2N, 8N that can be found in some libraries or purchased online that are invaluable for showing you every nut, bolt, clip, and assembly, how to adjust, etc (like the suggested comments below on the nuts to use on the manifold, pitman adjustment, and other things). Great job and thanks for the video!
FYI: There are three drain plugs on the bottom of your tractor, because your transmission, hydraulic system, and differential all flow together and thus use the same fluid.