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Well I went over the file, but most of the functionality is encapsulated in functions defined elsewhere. But the file did help some. I was reminded that WHM starts the service with the "-DSSL" option.
The directive in Apache is written as
<IfDefine SSL>
Listen 80
Listen 443
</IfDefine>
So that was the problem. It was causing it to try to listen to Port 80 for all IPs, and one's already in use, causing the issue. When I was using apachectl I didn't have SSL defined, that's why it worked fine with apachectl and not WHM's restart.
I just have to change that Define, replace Listen 80 with Listen [ip]:80 for all the ips available to Apache.
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Nobody doing nothing
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