Ah, someone who doesn't read the instructions! Too much in a rush to do the job the quick and easy way.
This is not the place to discuss this, but there is a simple way to sort this out. Identify all the core files you modified (hopefully by comparing file times, or by winmerge comparisons) and make them your override files by copying them to the relevant template folder. Then restore the original core files a few at a time to make sure it still works. What that's done, you're good to go with an upgrade. Do it this week. Really.
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