For further testing, I installed a fresh WP site and fresh copy of this plugin and imported from a folder. MUCH better. Any MySQL issue I had for adding in the database and loading a page is completely gone. So now I'm down to the following, which I can work around for the time being, but would really like to see fixed for future releases:
1) The image backup option always defaults to yes, even if I change it to no and hit save.
2) The permissions of all files generated being 600 instead of 644.
3) The disdain the plugin has for capital letters causing another directory to be created.
I can fairly easily run a script to take care of number 2, annoying, but at least it's only an annoyance for me. Hopefully this can be worked before others start making galleries. 1 and 3 mean a lot in the sense that multiple copies are needlessly being made, which would cause over double the space to be used on the server. I currently have ~64GB in gallery images so you can see how this would be an issue for both space and deleting so many files.
However, I must say, doing it fresh makes this viable for me to use on the main site. With the new ability to use nested folders, I would have had to re-arrange everything anyways to take advantage of this feature, which we really need and are grateful to be able to do so now. I'm going to be messing around with the short code stuff to see if I can get the formatting of the galleries on the pages to how it was previously, and it's great to be at that level of testing. Since this is looking much better than earlier in the month, I'll be doing the mass change over this weekend, and if it goes well, I am definitely going Pro!