Basic does not include the Combat Animation Enhancement. So there should not be any overlap there.
You aren't supposed to delete anything in item_kinds1...you just change the number near the top and add lines near the end.
As for editing module.ini, comment out/remove everything from the instructions that you can find. Some of the lines in the instructions won't be there. Make sure you add all of the lines noted.
See my response to this thread:
question about installing for some more pointers about installing.
Regardless, it might be best for you to "start over". Take your backup of Native, make a new copy for Floris Basic, and try adding it to that. If you've changed skeletons.brf for the Combat Animation Enhancement, be sure to include the file actions.txt from your working Native folder in your Floris Basic mod folder so it correctly references them. And if you make any changes to the module.ini for the animations, be sure those changes are present in your Floris Basic module.ini