I replaced the pump reservoir with a spare I had, it was leaking, and kept the stock box for now. If it gives out on me, it will get a PSC box, like the LJ. Blaine gave advice on how to sort out the fittings, which I just stuck with the 3/8" (-6AN) for now.
The 16" cooler is in, so all I'd need to do later is swap the -6AN fittings for the -8AN set I have in the box. Overall, I'm very happy with the entire setup (steering and transmission coolers). It's clean and done the way it should be. That said, it was a PIA to get everything right!
I was also able to get the new A/C condenser and Mopar radiator installed. I still need to connect the new hard line to the condenser, but I'm almost ready to put fluids back in it for the first time in 5 weeks.