Okay, apparently I missed irisheathen referring to the smoke being a -4 penalty which must be why all of you are doing it, but it is really a -2 which is what I have been using to this point. I went ahead and used a -4 on the shot the guy in the skylight made just now, but the best thing I can think of to compensate anyone for my missing this error until now is to give O'Connor and Johnny back two health boxes each, Clem hasn't been hurt, otherwise she would get them too.
From here on I will try to be more aware of telling you guys these kinds of modifiers, and moving forward the smoke is at the -2 level.
Once O'Connor takes his third and fourth passes, everyone can roll initiative again.