Ok well, doesn't look like any of those are fouled, really.
How about some pics of the bike all around (with focus on carb/engine area) so we know more.
Have you done the basic stuff recently?
3k mile tune up checklist
ever vac synced the carbs?
checked for air leaks? (how do you pressure test a boot??)
It's a good thing you made this thread, just about every hypotheses you had so far was dead wrong.
- Plugs are fouling (all four plugs not fouled, #4 in fact looks lean.)
- Carbs are "flooding" (nothing coming out of the overflow?)
-"I'm thinking about switching to 100s, but it seems a little lean for the setup." (not running lean overall, only possibly lean in certain ranges--unverified)
- Almost advanced the timing which wouldn't have helped at all
Don't take it the wrong way, pointing out the systematic troubleshooting and then taking the data and coming to real conclusions based on what we observe--this is going to be how you learn to troubleshoot correctly. Also, anyone else who comes along and looks at this thread is going to learn something from your post--so that's a great service to the community.
Most people ride their 550's around all the time with no real problem with some big bad "flat spot." It's unnoticeable or just not really a problem usually. You need to understand you have drastically modified your intake and some people never really get it right. If you're looking for the smoothest possible power band and want your bike to work as best as possible, get an airbox.
To go any further I think we need some pictures of your bike. Just recently a guy was asking for help and we get to the second page and finally see that his "all stock" has pods and 4-1, so he was just wasting people's time.