Using the recurse (-r) option to diff to generate patches is fine, but please take a look at the resulting patches to make sure you do not have any unnecessary junk in there. In particular, diffs between two backup files, Makefiles when the port uses Imake or GNU configure, etc., are unnecessary and should be deleted. If you had to edit configure.in and run autoconf to regenerate configure, do not take the diffs of configure (it often grows to a few thousand lines!); define USE_AUTOCONF=yes and take the diffs of configure.in.
Also, if you had to delete a file, then you can do it in the post-extract target rather than as part of the patch. Once you are happy with the resulting diff, please split it up into one source file per patch file.