Hey dafebe,
You say you downloaded joomla_index_patched_1_0_12.zip
The index.php file that is in that zip archive has been patched by Wolverine (as you know) and is intended to be uploaded to your server, overwriting the original Joomla index.php file. Once you have done that (uploaded and overwritten the index.php file with the patched one) you should be able to go to your Joomla admin for the bridge component...install... to see see that the green "done" link is now there for the patch source file step. i.e. now that the patched index.php file is on your server, the bridge will see that step as completed (files are patched).
If it still doesn't work, it may be because your server permissions are set so that you're not actually overwriting the file. In that case, rename/delete the orginal index.php file and then manually upload the patched file to replace it. Make sure the file permissions are set correctly 0755 or 0644 etc (depending on your set up). My host has a very restrictive permissions set up and I always run into problems with scripts that try to make a backup of a file before a change is made (like patching and unpatching)...
As far as the SMF patch you talk about, I'm not sure what you mean by that...
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