I originally was writing this post as a question, but figured it JUST as I was about to post
After installing the Network Agent there is a like on how to import the certificate into the app which doesn't work, so your left flying blind
So you can get a little bit of a catch 22, after following this KB and getting my certificates in order I discovered that I was still getting blocked, spent AGES creating new certificates importing them only to have them fail in Safari.
To resolve this go to Settings-> General -> About -> Certificate Trust Settings. Then just trust the root certificate
Once I did that I could log into the User Portal in Safari and download and install the .scc file into the Network Agent!
Hopefully this will help someone who comes across this
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