I only jump started the process. Many folk on this thread have offered advice about how to streamline it.
To answer some of your questions . . .
1. The Link2SD program should only copy the files to your second partition, which is located in the data/sdext2 folder. You shouldn't see a duplicate copy on /sdcard.
2. I'm not sure about the intsdcard directory. I don't have anything like that in /extsdcard. That sounds a little weird . . . you said the internal storage files are there?
Anyway, glad to hear it's working!