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well everything that you mentioned in your paragraphs could be solved if you RTFM. There is a detailed help manual built right into the WHM sidebar. Look for it, you no longer have a reseller or shared account so domains don't have to point to a subdirectory anymore.
Your site got canned because of shear volume, it happend to me and I went dedicated. I am not extremely knowledgeable about WHM myself but I RTFM and haven't had any issues.
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