You're welcome! Some of these patches are a real pain in testing.
At least editing the patch file to skip the .htaccess file patch and then editing your custom .htaccess copy to deny access to cron.php is is a pretty simple step.
One of the biggest fails on this patch routine is hunk failures because one of the files got uploaded without line ending translation (binary mode) and the SFTP client didn't translate line endings. The file will have MSDOS CRLF line endings instead of *nix LF endings. Most of the time, extracting a file from the Installer Archive and overwriting the file will cure it, stinks that this didn't work.
On *nix there's a file called dos2unix that can be run, or you can re-save the file out of TextPad as a Unix UTF-8 file before upload. I've had to do that on patch files as well, they're a shell script and must have LF line endings only!.
I know this is after the fact, but put here for future reference.
