Phase refers to the yokes on the ends of the driveshaft, are they in the same orientation or 90* off? To reinstall just put the t-case in neutral and rotate the flange until it lines up with the driveshaft yoke. Make sure to put the e-brake on.
Did you leave some of the plastic geared cable inside the motor from the old antenna that maybe snapped off? You could find the chrome cap maybe from someone parting out their truck here in the classifieds.
I used JB Weld epoxy with metal in it and either it didn't work or I didn't go heavy enough because after two years, in the heat of this summer the case peeled open. Went with the full Aisin replacement assembly this time instead.
If it's coming through that much, I'd have someone pour water moving slowly around the perimeter of the sunroof while you sit inside at see at what point you see water inside.
EFI thread was posted one up from that and he said he'd tried it. OP, I'd maybe look at an advanced scanner or Techstream to see if maybe you're getting misfires and see if there's a count of those while running.
His post said it's not. You may have two leaks going, I think you've also got a leaking CV band that's throwing grease (spray pattern). I'd clean both well and see what returns.
I would wipe the areas down and inspect regularly so you can get an idea of how much fluid is leaking out and at what interval. For the valve covers, many have had success with just slightly tightening the cover bolts, careful not to over do it and snap them.