Upgrade to 6.0.3 issues

Hi, I am trying to upgrade from 5.2.2 to 6.0.3. After the upgrade had run and I refreshed the templates and published a site, I found a couple of major problems.

1) The upgrade had replaced my customized indexes with the default indexes sans widgets, etc. and at first they would not display.

2) When I clicked on the continue reading prompt on an entry, I would get a 500 server error.

I went in to check permissions, and I found that index.php had a 666 perm instead of a 755, and when I changed it the index displayed.

The same problem exists at the archive level as all of the archives are 666.

I did not do anything “weird” in the config file. In fact, all that is changed is the database info, static file info etc for a normal installation. Below is the procedure I followed to do the upgrade:
1. Backed up EVERYTHING
2. Created a copy of the mysql database for the new MT version
3. Uploaded MT 6.0.3 zip to the server and did an extraction into its own directory (mt603).
4. Logged into MT 6.0.3 which took me directly into the “upgrade” routine.
5. Logged into MT 6.0.3 and did a template refresh on the first blog.
6. Published that blog.
7. Looked at the blog and got 500 server error.

• checked file permissions. the files were set to 666 instead of 755 so changed the perms to 755
• tried accessing the blog again and it came up with the default templates and all customizations missing.
• tried accessing the “read more” and got another server error.
• checked perms and once again they were wrong (666 and changed to 644) - that worked for those entries, only 19752 to go NOPE!
• Replaced the default index file with my old index file to get my customizations back, but that doesn’t resolve the other issue.

8. Went back and logged into 5.2.2 and republished to get everything back the way it was BEFORE the upgrade attempt.

So what did I do wrong? Or is there a problem with 6.0.3?

Thanks for any suggestions.

rowan