The upper and mid rod end bearings are in and adjusted but I can?t get the threads on the lower one to engage with the nutplate. Any ideas? Does it look like I?ve damaged the nutplate thread?
Sometimes nutplates shift just enough during installation to keep a screw from properly threading into them. One thing you could do is remove the nutplate and very slightly enlarge the hole for the bolt. Or try re-installing the nutplate using a bolt threaded into it to hold it in alignment, perhaps with a new nutplate.
Just run a tap in enough to get the threads started. I had to do that on one of mine. You don't want to completely tap it and loose the locking capability in the nutplate.