What happened to the mutator?
Version 2.00 of UTR is no longer a mutator. What seemed like a good idea at the time probably wasn't. A mutator is all about modifying the UT's game characteristics. UTR doesn't do this, so really it shouldn't be a mutator. Instead its just a plain old UT chunk of code. There is an upshot to this, any effects that UTR was having on NGStats logging have now been removed.

Why does the reporter keep leaving IRC on a map change?
Sorry to say but this is just one of those things your going to have to live with. It would appear that the UT server reloads its server based package at each map change. So unfortunately there appears to be no way around this.

Where's this web admin then?
Assuming that you modified the ini file according to the installation instructions and you have UT's web admin enabled, then you can access the UTR web admin on the same IP and port but with a suffix of /UTR.
So if your normal webadmin is on http://123.456.789.001:28100/ServerAdmin
Then the UTR webadmin will be on http://123.456.789.001:28100/UTR

So I've got web admin, what is the username and password?
The username is always UTR. The password will depend on the type of access you want (see the next section).

Passwords, adminstrators, reporters?
UTR allows for two types of users, Admministrators and Reporters. An Administrator has full access to the entire functionality of UTR. A Reporter only has access to those functions which immediately report a score / spectator list.
Both passwords can be configured by an Adminstrator through either the IRC interface or through the web admin interface. The Administrator password is totally separate from any other UT passwords.
What this means is that you can give a few people Reporter access to UTR to enable them to generate score information on the fly, or to broadcast individual players scores during a team game, without them getting access to the administrative functions. When using the web interface, a Reporter does not get access to any of the Administrator web pages.

Commentary and scoreline channels, what that all about?
A commentary channel is one in which the scores and also kill / cap messages are broadcast to. A scoreline channel will only ever have score information broadcast to it. So why the difference? Imagine a league night with more than one concurrent game ongoing. You can configure UTR to broadcast commentary for each game to their own channel, say #league.1 and #league.2, then configure UTR to broadcast scores for those two games to a common channel, say #league.scores. With this sort of configuration you can have everyone (including league admins) view all scores for all games, and leave it up to the individual spectators for them to choose which game they want to see commentary for.

Why only DM, TDM and CTF?
The way in which the UTR works is to programmatically check UT events from within the game. This is the advantage that UTR has over external reporting bots (ie it never gets the score wrong...). However, because it works in this way, the code needs to check for special events that occur for the different game types. Having not had the time to cover all game types and mods I just did the top 3...

UPDATE BY WEBSLINGER: I added DOM :)