Most mods won't work (it depends whether the mod altered the galaxyscenario I believe) and I don't think you can down grade back 1.1.
I'm afraid many more files than this were changed. Chances are any mod that added content (I.e. the vast majority of them) will be obsolete. Only smaller mods like voice/music/texture replacements or ship rebalances might still work.
If this is the case is there anyway to downgrade sins to 1.1 again?
Not unless you already had a backup made I'm afraid. Steam likes to keep everyone on the same version... 
