I decided to take Tejas' suggestion and do some running around in the Cordon before going to visit Sidrovich.
In the process I think I broke the main story line. I haven't been to see Sid yet, the military are pretty much dead throughout the Cordon. I've done all the sidequests I can find. Most of the Stalkers at the Embankment are neutral/friendly. And I can't get into Sid's bunker.