1. My tune up history for the bike is when I got it, carbs were cleaned and rebuilt, new air filter, new spark plugs(matched with stock numbers), new intake valves, new head and base gaskets...and just the standard cleaning of everything.
FYI; Part of the tuneup ( 3000 miles/6 mos), is gapping the points, checking/setting spark timing, tappet adjustment, cam chain tensioning, and cleaning/replacing the air filter.
2. Yes, correct sparkplugs, I dont know the numbers off hand, but they are matched with the book and also same numbers as previous plugs in there.
If there is an R in plug number it's the wrong one and the standard plug for a 750 is NGK D8EA which is too cold for the 550 and won't allow the plugs to self clean unless you drive it 80 mph for 30 minutes on a 100 degree F day. I've found several Cb550s with the wrong plugs installed and had parts counter men sell me the wrong ones for this bike. But, if you're confident about your plugs...
3. Not stock air filter. It is an aftermarket foam kind...but that would cause it to run leaner...
No. Not if it was over oiled, packed too tightly or clogged with dust etc.
Do the test where you temporarily REMOVE the filter, and tell us if the run symptoms change.
5. And yes, I was reading the correct part of the plug...black in color by the way
Base ring black is okay, center electrode insulator black is not.
6. No, jets werent drilled
Never in the bike's history? How did you measure them?
7. Idle air bleed screws are out 1 turn
You're side steping questions. That's fine if you wish to side step issues. But, the wrong bleed screws can seriously screw up mixtures. If they are the stock hollow ones they are set on the rich side of the stock adjustment range, which by the way, is now likely irrelevant with the filter and exhaust changes. If someone put air bleed screws in there from an F model bike they'd be solid and way more sensitive to adjust. You'll need to find the proper idle air screw setting for your non-stock setup.
8. Yes, still stock main needles
Okay, I believe you didn't change them. Do you know they are original to the bike?
9. Yes, floats are shutting off fuel correctly
10. have not measured fuel level in bowls when fully filled, but they arent leaking and seem to be shutting off fine
High fuel levels will richen up the entire range of carb operation. This is a carb fine tuning aspect, and not simply pass/fail.
11. New gas lines, fuel filters, and tank has been cleaned
12. Dont know
What? And, you won't bother to look at your bike? Am I to assume you don't care either? If you've only had it for a year. How do you know you have the original carbs on the bike?
13. Havent removed emulsion tubes
Clogged emulsion tubes will deprive the air premix before injection into the carbs causing a rich condition while operating on the mains and slide needles.
So far, this is what I can tell you. Just seems odd to me with those aftermarket turnouts without baffles that the plugs would have been running dark. Also seems odd that adding a 4-1 baffled MAC exhaust would restrict the air that much and make it run that much more rich to foul all four plugs in such a short distance.
I believe you are barking up the wrong tree blaming the exhaust for your running rich problems. For as long as you have had the bike it has run rich, so you tell us, and changing the exhaust didn't impact that trend. More likely you have an air filtration or carb cleaning/tuning issue, I think. But, hey, what do I know?
If you don't want to seriously address the checklist I provided, that's certainly your option. I'll step aside and let others help you. Perhaps others will provide you with the information you want to hear and in form more pleasing.
Best of luck!