I'm not familiar with all of these, but it looks like you could just reinstall most of them without risking any data loss. Particularly if you make sure to reupload the files and just reimport the products like you would during an upgrade. I presume you've double checked to make sure all the files from the modifications got moved in the upgrade? Even made sure to check any special instructions that each modification may have had that you may have overlooked when moving them?
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