Why not simply use MirixV2?
http://planetquake.gamespy.com/View.php ... il&id=1734
It's a neat little frontend that's pretty easy to understand and lets you rotate or mirror/flip a .map file and automatically swaps textures by filterlists you have to enter manually. It comes with a predefined filter for almost all ctf textures that come with the original game. It's even possible to swap coloured light entities to different colours.
It comes with a readme, which should first be investigated.
If you have something in your map that you don't want to be handled by Mirix (e.g. a already finished assymetric middle) seperate it by selection or clipper, save it it to a different .map file and later copy/paste it back to the file that Mirix did output.
I love that tool, it's so fast and easy, great invention.
Edit: The only problem I had with it at first was a misconception. A false understanding from my side or them of the words "around" versus "along". You'll find that out for yourselves. Just make a backup before you have your first attempt

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And Edit2: it can even come in handy for FFA/TDM maps. If you had some trouble 3-point-clipping some geometry of a doorway/hall/whatever and want the same geometry on the other side and can't simply clone/rotate it.... look no further.