Now that you have CWM v6046 already on internal memory, it is ok to have the files you want to flash on the external SD. It is only the version on SD that needs the files on internal SD. Get SDFormatter free on the web and use it to format the SD so it goes back to its normal size. Then you can put the CM and gapps zips on the SD. CWM v6046 has an option to flash a zip from external SD.
But that being said, that error message tells me that you have too old of a version of CWM on internal. Are you sure it is version 6046?
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