Hello && Welcome @fffhurst
If you could please be Be Patient the community members here have full time jobs and we help here on our own time so if you post was over looked it probably because of the lack of information.
Ok so I’m going to pick your post apart.
You defiantly may have a issue with certificates. How and where did you make these certs for your inputs.
If the input on Graylog do not show running , but able to see message your issue would be from there. Knowing that all parts of your Graylog server is functioning correctly is the fist step.
Seeing your full logs would help. I cant fix a CAR if I don’t see it 
. Logs give us the ability to solve these issues. This is probable a couple issues, Disk space permission or the Graylog configuration made etc…
Perhaps check here for anything that may pertain to this issue.
Your Graylog config file maybe incorrect, showing that would be a start and please substitute any personal information while using the markup this is shown in the text box. If your unsure please look here for further information.
That would be your Input, Lets say someone is trying to put a round peg in a square hole.
What you have here my friend in the incorrect INPUT for the type of log shipped. This would be good information to know on how you setup your environment.