You should just let certsagenc.php keep using the same CertSage data directory that you were using before. Did you modify the permissions in the lines I mentioned above? That should give you the necessary permissions to download the files. I'm going to make those permission changes in the official next release BTW. Thanks for shining a light on that.
Well, that's interesting. I changed the permission value in the lines stated from 600 to 644, which, I believe, is rw-r--r-- then uploaded certsagenc.php and (when I ran it) specified www.fractal-timewave.com and fractal-timewave.com as the domain names. (Do I need to do both? Can I add another domain?)
CertSage reported 'Success' and the certificate file and four others were saved in X\CertSage as follows: certificate.key, certificate.crt and response.txt file had permission 644, and account.key and code.txt had permission 600. I tried to download all five to a folder on my site but only the two certificate.* files and response.txt came over. My ISP says that to install they 'need the .KEY file, the Intermediate file and the SSL certificate." Since, so far I have downloaded just three files; that's probably not enough for my ISP. Maybe I should change the permissions from 644 to 666 or even 777.
In certsagenc.php I changed the permissions to 666 rw-rw-rw- then reran it. I got "Success!" again but the only difference from last time is that the files in X/CertSage (where X is the directory one step up from my website root directory) is that the files which had permission 644 now have permission 666. So the files I could download to my site are the same as before.
Correction: Permission 666 is -rw-rw-rw.
Actually its: rw-rw-rw-
The leading "-" is not part of those numbers:
-rw-rw-rw-
777 is:
-rwxrwxrwx
I see you are removing the last dash as insignificant (instead of the first one).
The first space is for "l" links or "d" directory, etc.
For "fun" look at:
ls -lR / | grep -v '\-rw\-r\-\-r\-\-' | more
ls -lR /dev | grep -v '\-rw\-r\-\-r\-\-' | more
As a DOS/Windows programmer, it's about as much as I know that the first position is "d" for a directory, or "-" for a file, then follows three triplets for 'user', 'group', 'other, and ... you know. Mostly I don't need to know, except in cases like this.
I am pleased to inform y'all that by using SertSage I was also able to get an SSL certificate for my other website. Of course, I had to ask my ISP to install it, which it did with no fuss. You can see the desired padlock at www.hermetic-systems.com
Many thanks to the (@griffin) Griffin, author of CertSage.
For how long are these certs valid? Will they expire after 3 months (as those from ZeroSSL do) requiring me to renew them?
Yes, all (subscriber) certificates issued by Let's Encrypt are valid for about 90 days. Let's Encrypt recommends renewing them after about 60 days.
Let's Encrypt highly recommends automation wherever possible to avoid repeated manual actions. With your current workflow it looks like that's not possible.
I am very happy to hear that you were able to get your certificate working with CertSage. 
Sorry I wasn't responsive for a few days. I've been out of town for a funeral and haven't been able to check-in much.
I have been working on improving CertSage for the next release and have heavily taken the events of this thread and another thread into account in my streamlining efforts.