Let's do the nut first. The nut was tricky because it's a metric M12 x 1.5. 12mm nuts are fairly common around here, but the 1.5 thread is not. Most hardware stores in my area like Lowe's, OSH and TrueValue seem to stock the coarser 1.75, both in regular and nylock. I had given up and was going to order a stupid nut on the web until I happened to be in the NAPA auto parts store in my town and viola! They had it! So now my transmission is firmly mounted on both sides with the correct nut, and it won't work its way loose.
Now onto the transmission shift linkage cover. I didn't remove one from the car during the teardown, so I was searching around for a used one or a replacement. I finally stumbled on one at Auto Atlanta. I ordered it for about $25, only to be notified it was on backorder. I waited for about 2 months for it to show up, and sadly it's not very good. First, it's just a tiny bit too small, so it's extremely difficult to get around the linkage housing. Second, it's made from very thin, brittle plastic so of course in my efforts to get it to fit, the lip cracked off. I called up Auto Atlanta and the guy seemed to know exactly what I was talking about when I described the problem and my feelings that it's just not a very good product. He explained that they can only get this part from a single supplier and they know they have problems with his size and material choice. He readily gave me an RMA to ship it back to them.
Shortly after all of this I was looking for another part and I found a freaking transmission shift linkage cover in a cardboard box of parts from the previous owner! Argh! I installed it, using a hose clamp around the lip and it's great. It looks like it was painted at some time in the past, so I'll remove the paint and get back to the original plastic and treat it with some back-to-black plastic lotion.