Pod filters

Since I got the bike running on all 4 since my last post (clogged pilot port in carb 1) I've been battling the trouble of pod filters. (Bike didn't come with air box). Pilots are stock and mains have been drilled to 96s.  Air fuel screw caps have been removed (TK-22 carbs). The bike is definitely rich. Black plugs and It's very easy to start when choked and I can turn the choke off right away and the bike will idle. Additionally it starts easier/with no choke when the engine is cold. It will idle but it' gets worse as it warms. I took it for a little rip up and down my street, as the bike warms it runs worse and becomes hard to start. Regardless, it's very rough coming up from idle when given throttle. An 1/8 turn of the throttle causes the bike to cut out. If I catch it right it'll rev up high with seemingly no issue. I've played with the air fuel screws, from 1-1/4 Turns out all the way to 3 turns but there's seemingly no change. All throughout my trouble shooting the bike has and still seems to get very warm. Is it normal to the motor to get very warm on these 550s? Is this another symptom of running rich? Dynojet says that these bikes don't really need pilots re jetted on their website, but I'm not opposed to going up on them, I've been skeptical to drill as of now because the fourney 60239 #61-80 drill bit set I got that Lou recommended on his site all measure to contradicting measurements with a pair of calipers. Bits #80-76 all measure to just about .5 mm +-0.8 mm. (Will bring bits to work to measure on a higher end caliper) Baseline numbers I found for pods seem to be 100 mains, 37 pilots, and shimming the needle with a .78mm washer. I have the washers to shim, should I try this before I drill the pilots? My understanding is shimming the needle will cause the bike to be richer though. Another question is can the stock needles be shimmed. It's to my understanding that there are no clip positions on the stock needles. Regardless, I drilled the mains because I know they'll need to be drilled with pods. Anyone have any insight on the next steps. I know it's tough given there's some variance in altitudes and temperatures depending on where you live. How much does this actually effect the bike though? I'm in Upstate NY for some reference enjoying the rainy weather... 

edit: I've also heard of people taping off or restricting the air flow of their pods. Im not opposed to this either as it could just be the easier route. I'd rather not spend the money on an airbox, and I'm not sure if it'll fit with the battery and electronic tray I made. Anyone ever try this method and have any insight on what's the best way to go about it?

"lean" not "rich" causes a motor to run hot - Pods cause lean running not Rich !

I am of the opinion that not all pod filters are created equal. What brand / type are you currently using?  Some have a lip of sorts that either cover or alter air getting pulled into the air jets in the bell of the carb. Others do not flow any more air than a stock air box / filter do. Some actually flow less that the stock set up.

The TK 22s use a spring controlled choke flap and there have been known issues with them. Some of the issues you described re starting are due to the choke system and the fast idle setting is also related to starting issues .At least that is my understanding .
 

The plugs are black as the night sky. Even letting the bike idle with no filters and new plugs they are black which tell me it's rich even though everything is favoring the bike running lean. This was done with air fuel screws a turn and a half out to keep it close to factory setting. 

Maybe it's excess carbon build up on the plugs I'm seeing. 

would being lean cause the bike to not wait to rev up from idle? Or is this more of a jetting issue? 

Not sure of the brand of pods on it either... Picked them up at a local swap meet but they are not restrictive at all.  

CV carbs tend to be really sensitive to airflow changes on the intake side. Running them without any filters will introduce more running problems than you can shake a stick at. To tune the carbs, you need to use the full setup that the bike will be ridden with, or you will end up chasing your tail.
Some aftermarket filters are so poorly designed that it is nearly impossible to get the bike to run at all, much less to run well.

APE, K&N and Uni make good filters.