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Well, that sounds like two issues: one with viewtopic.php or include/functions.php (the admin tag).
Check the usergroup permissions first

OK.
You just want to add the following code

update_forum(number);

where number is the ID of the forum where the topic is. This assumes you've included include/functions.php somehow (most likely using include/common.php)

Which has been fixed in 1.3 for some time now

connections != queries
Long lasting connections can cause an issue, yes, but the issue is much more likely to be host restrictions to cut down on one person hogging the connections.

include/functions.php, error function

As Paul pointed out, PunBB supports both PHP 4 and PHP 5. I can't think of any features we've decided not to implement because of PHP4. So, it doesn't make sense for us to limit PunBB to PHP5

Userlist isn't possible without a mod I believe.

I don't see any of that code being used anywhere in the code you just pasted

echo '<img style="vertical-align: middle;" src="'.$pun_config['o_base_url'].'/img/'.$pun_user['style'].'/blog_icon_dot.gif">';

There are a couple reasons the code you had wouldn't work. This code should work fine, assuming you're inside a block of PHP

mmm, I should probably have mentioned this, but user_id doesn't exist: poster_id is what you're looking for

Both users and topics should be a left join

That's not the reason you can't optimize it, you can't optimize it because it's a HEAP table and thus doesn't require optimization.