First of all, nice looking bike and congratulations and welcome to the SOHC4 forum! Lots of 400f riders here so you're sure to get plenty of good advice.
I'd say you probably want to get a new brake piston. Once that hard chrome is eaten through it really doesn't clean up very well. And replace the o-ring in the caliper (make sure to clean out groove!), and while you've got it apart make sure that the pivot arm moves freely on its shaft as it should, and may as well lube it up. There are two o-rings, top and bottom, so make sure to replace those or don't loose them if they are in good shape.
Can't quite tell from the picture, but do you have a stock airbox? Looks like maybe not. Without it, it can be hard to tune carbs but it can be done. As far as the chugging, what RPMs are we talking about? These bikes like to rev and if kept in the lower RPM's you will most definitely carbon-foul the plugs and combustion chambers. I have mine above 6-7k constantly. But you're right, having 1 and 4 present like that would lead me to think perhaps a weak spark out of that coil. Could be bad plug caps, points, wiring connections, etc.
There are just so many things to look at, though, so before I went too far with trouble shooting I'd go ahead and do a full 3000 mile tune-up. valve adjustment, oil and filter change, cam chain adjusted, timing rechecked and set with timing light, air filter cleaned/replaced, carbs cleaned and synchronized (since you're in there already). Make sure to check your float levels in your carbs as well as all the air passages, and remove and clean the emulsifier tubes. PM me your email and I'll send you a great step by step how-to for rebuilding cb400f carbs with pictures (courtesy Yahoo cb400f group).
