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I'm not sure if this will help you or not, but I just installed an SSL certificate for FileMaker Server 13 this week.
My situation was a little different from yours. I ended up generating the request and getting the certificate through my Web hosting provider (MediaTemple). That made the process of generating the request, and purchasing the certificate, a little easier. It might not be any easier for you.
The problem was that, by ordering the certificate through MediaTemple, I couldn't use the certificate request file and encrypted private key file that would normally be generated if you were to generate them with FileMaker Server itself (via the "fmsadmin certificate create" command). So when I received the certificate, I ended up having to copy it, and the certificate request and encrypted private key files, to the directory that FileMaker Server expects them to be in, and renaming them. Instructions on how I did all of that are here.
Anyway, my point is that you might want to try to purchase an SSL certificate in a way similar to how I did it.
Hope this helps. If you have questions and want to PM me, please feel free to do so.
I was finally able to get the certificate installed using the command line tools as outlined in the FMS 13 security guide. It turns out that the reason the key file and certificate mismatch was being caused by a certificate in the wrong format. Once I downloaded the X.509 format from my GeoTrust account, it installed properly.
I appreciate your taking the time to let me know what worked for you. In any case, I believe FM needs to update their documentation with more specifics so that we don't have to figure it out by trial and error.