I solved this issue, well, it turns out there was no issue. I successfully signed and released an app even though the certificate I used to sign it was 'untrusted' and had no root certificate. Neither of these issues prevented the certificate from working as it should.

Thanks eskimo, I've emailed support and requested that they revoke one of my developer ID certs, or increase my limit above 5.

Seeing as Apple are in no rush to help me fix this issue, I am going to have to create a new Apple ID, pay the $100 to create a new apple developer account, and sign my apps with this new apple ID/dev account. My question is what could potentially go wrong with creating a new apple ID, then signing out of my apple ID on my mac, then signing in with the new ID? How does this impacts certs etc? Is it better to factory reset my mac then sign into it with my new apple ID?