I assume you want something like:
file001.jpg, file 001.CR2
file002.jpg, file 002.CR2, etc
and you are getting file001.jpg, file002.CR2, file003.jpg, file004.CR2, etc.
Try filtering by file type (library -> filter bar -> metadata -> file type) to select all the files of one type, renaming those, then selecting all the files of the other type and renaming those the same way.
If you take care to run the filter on exactly the same set of files each time (and of course preserve the file suffix while renaming and starting the number sequence at the same point) then you should have what you want.
I've not tested this, so I suggest trying it on a very small number of files at first.
However, I don't see the benefit of importing both jpg and raw of the same image.