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So your forum is at
http://www.mysite.com/forum
And the file is at
http://www.mysite.com/forum/12_to_1214_update.php

Moved to Modifications

Yes, I'm familiar with what the install form looks like

http://www.suffns.org.yu/forum/
You don't even have a forum folder in your website. You can't just name a random folder forum and expect it to work.

There's nothing to install on your computer: all you need is the ability to upload files

You uploaded the files into the /forum/ directory? Not into, say, /forum/upload/?

update_forum function in include/functions.php

And it is added in 1.3 as far as I can see: check for yourself
As I said, PunBB.org runs an unmodded copy of PunBB: you're not going to see a mod installed on this forum

This should also be possible in PunBB 1.3 with an extension (say, one that controlled avatar permissions for a usergroup)

Moved to Integration

There are various ways to do what Rickard is trying to do, which is integrate users from PunBB with trac without modifying PunBB:
http://www.trac-hacks.org/wiki/DbAuthPlugin | You'd need to maintain a Trac auth table in addition to a PunBB table
mod_auth_mysql for Apache is another possibility, assuming you have access to a version which supports the password hashing you're using

PunBB's tables have names like users, posts, etc. You can set a db_prefix (set in config.php) which is prepended to table names, allowing for multiple installs in one database. So, if pbb_users is your PunBB users table, you need to edit your config.php file and set $db_prefix to pbb_

The higher number in select_full_join is caused by the poorly optimized query: again, until you can figure out why your setup messes up the way it does, there isn't really an easy fix