Yes, track ends and fenders are a pain. Some tips:

If you get some M5 wingnuts, you can make your fender quickly removable without tools. See this page: http://www.phred.org/~alex/bikes/quick-release-fenders.html

If you know where the puncture is, don't take the wheel off. Just unseat the tire bead enough to pull out that section of tube and patch it.

You can install the wheel wobble-free in one shot by "walking" the axle back. See http://www.sheldonbrown.com/fixed.html#wheel. Note you only need one wrench to do this. I've never had a use for chain tensioners, but some people swear by them. Ditch them and see how it goes.

It would cost you ~$100 to have normal horizontal dropouts installed by a framebuilder. Maybe worth it to you.