Hi @Daniel_Bliss. There is a very simple process to easily correct this. It will involve exporting your entire list, via the Export action. When you export, you will only need to select the ID (Infusionsoft Contact ID) and the Company Name fields, to export.
Once you have exported, you will be able to head to your Admin>Data Cleanup area, to perform what is known as a Modify Existing Records Import. From here, you will upload the file you have just exported, and go through the field matching to ensure that the ID field is matching to the Infusionsoft Contact ID field, and the CompanyName field is matching to Company, in the dropdowns.
When you reach the next stage of this Existing Records Import, there will be a box that you need to tick, telling the system to create a company record for these contacts, and attach the contact to it.
Now, you may ask, what if some of them are already correct. That will not matter. The system performs a case sensitive search, before creating a new company record to attach the contact too, so any contacts that are already displaying correctly, will remain as they were, and only the contacts that are not attached to the company will be modified.
I created a really cool visual of this whole process that you can watch https://www.screencast.com/t/IvJQY8Y3 I go through the steps of exporting my list, and then show how to import, via the Modify Existing Records, import, and the option that you need to select, on the last step of the import process.
I also wanted to share a help article that talks a little more about the Modify Existing Records import, for reference. http://help.infusionsoft.com/userguides/contact-management/import-contacts/mass-update-contacts-with-a-spreadsheet