We've just done a similar route to yours in 2010 and are currently trying to get through the flooding in southern Thailand.
Obviously a lot of countries to go through and my internet/electricity connection isn't great so I'll be very brief. If you go the 'borders' section on our blog you should get an idea of what paperwork requirements you can expect.
As for security, i wouldn't worry about it too much (it's easy to do when watching the news!) but obviously be aware of things. The chances are you won't encounter any hint of a problem on your route. As for visas being issued, just make sure you've got Iran and Pakistan sorted when you leave and the rest you can pick up on the way.
Don't worry, you'll love every second of it.
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