It turns out that it isn't a simple matter of copying files. While the files I used for downloading can simply be copied over, with the main time involved being creating a new link on the new website, the files used for reading online require hands-on editing for every individual commentary. It just takes too long.
Therefore, I've decided to forego copying those files for online reading. I will bring over just the files for download, the PDF files. Since these can be read online as well as downloaded, they really can serve both purposes. It will still be a gradual work, but I hope I can migrate a whole chapter every week or so, and be able to retire the old site by the end of the summer. I have already migrated the remainder of Chapter 1, and all of Chapter 2.
Just a word more: You will notice, as I bring over these older files, that they look very different from the commentaries I am currently creating. Mostly, I have evolved my formatting considerably, simplifying it and making it easier to automate. I no longer use colors, and have found ways to indicate all the different nuances within the commentary (emphasis, quotations, etc) using only black type. I am not prepared to take the time to modify these older commentaries to the new format; the content is there and is good enough, I believe.
Thanks to everyone who has supported this work!