There are several possible scenarios. Here are a few:
1) The 'Pending Request Not Found' error appears as if you are attempting to install a certificate that does not match the private key (Pending request) that is currently residing in the Certificate Wizard.
Microsoft IIS 5 and 6 only allow you to make one request per site. If you create a new CSR for the same website, your original request will be overwritten. If you have a backup of the private key, you can install the SSL certificate via the MMC if you can restore the request to the REQUEST folder.
If you are not able to find the matching private key for the certificate, you will need to have the certificates re-issued by submitting a ticket at our support site.
2) "The pending certificate request for this response file was not found" means you do not have the 'request' the CSR was generated from.
Without it you will not be able to get SSL working on your server.
3) If you are generating the CSR and not removing/deleting the pending request, but still seeing "The pending certificate request for this response file was not found" (or 'Pending Request Not Found') then you have a server side issue with IIS and should contact Microsoft for support on that as somehow the request is being removed/deleted.
4) Please make sure you are using all the latest IIS and Windows updates.
"Are there other issues that may be causing the " 'Pending Request Not Found' like common name not matching or using my servers private IP?"
Nothing that we are aware of gives the error you are seeing except those mentioned above.