First off here are some good links to help you with this.
https://devcenter.heroku.com/articles/ssl-endpoint
https://gist.github.com/shripadk/552554
https://www.resumonk.com/blog/setup-ssl-certificate-heroku/
I reissued my SSL cert and when I got it in an email I copied the whole thing not just the Cert information.
Afterwards Heroku ran the update without issues.
server.crt
Web Server CERTIFICATE
-----------------
-----BEGIN CERTIFICATE-----
MIIFKDCCBBCgAwIBAgIDEet1MA0GCSqGSIb3DQEBBQUAMDwxCzAJBgNVBAYTAlVT
IWAr5kQ/k2Hy4jXxHpqWMbK/SNu/UIlJM/xjyVvANy43orc2zBnGIPrzECMBWAP1
Xbkz4PUm4DuD8bRrkN7q9VKrssROFXkrl/teOg==
-----END CERTIFICATE-----
INTERMEDIATE CA:
---------------------------------------
-----BEGIN CERTIFICATE-----
MIID1TCCAr2gAwIBAgIDAjbRMA0GCSqGSIb3DQEBBQUAMEIxCzAJBgNVBAYTAlVT
knYYCnwPLI6FoOpC+ZNmZzYV+yoAVHHb1c0XqtK
LEL2TxyJeN4mTvVvk0wVaydWTQBUbHq3tw==
-----END CERTIFICATE-----