Hey all,
We have been able to resolve this problem and just wanted to give you the solution in case anyone else runs into a similar set of problems. This is for applying an SSL certification to CATALOG via a keystore using a self-signed certificate that was created via a Microsoft Certificate Authority.
1. Receive original certificate in our case this was a .cer file.
2. Import .cer file into the server's certificate store (run -> certlm.msc).
3. Export .cer file into a .PFX (make sure to include the entire certificate chain in the export). Define password. Save.
4. Take the .PFX file and dump it into the Service Catalog folder.
5. Right click and run as administrative the usm file for windows command prompt located in the Service Catalog folder.
5. Convert the .PFX into a .JKS keystore for Catalog to work with. This can be done by:
keytool -importkeystore -deststorepass changeit -destkeystore <hostname>.jks -srckeystore c:\certs\<hostname>.pfx -srcstoretype PKCS12 -srcstorepass changeit
6. Verify the import with the following command:
keytool -list -keystore <hostname>.jks
7. You should see a similar result as this:

8. Extract the ROOT certificate from the original .CER file by selecting it out of the chain. Export via an x509 which should export as a .CER file. Dump this file into the Service Catalog folder.
9. Import the root certificate into the keystore above using the following command:
keytool -import -trustcacerts -alias root -file c:\certs\rootCert.cer -keystore <hostname>.jks
10. You should see a similar result as this:

11. Add the variables indicated in the SSL setup instructions into the server.xml. I did not require the use of the keyAlias variable with the HTTPS string.
12. Test your ability to load HTTPS.
This resolved my problem. Thanks to Jason_Wolfe for doing the ground work.