Welcome and stuff.

YS1 is the stock B16A2 tranny right? Yeah, that's it I think. It's not the original though. Previous owner said he had to change it. I need to change the differential in it soon and change the fluid.

Once I tune this beast up, change the oil pan, change the differential and tranny fluid, the drivetrain will be in perfect condition. Then I just need to fix everything else and I'll be good. This car is one heck of a project.

Question. One of the previous owners was a major ricer (I have heavily de-riced ole Midori) and he cut out the grille (the honda H emblem). How much does this affect my aerodynamics? Would I notice any difference if I either added mesh (Type-R look) or put a new stock grille in? for that matter, does my Carbon Fiber Mugen Lip help at all? I have it mainly for looks cause my car is just funny lookin without it. And one more question. Do my fog lights hurt aerodynamics much?

off the top of my head I would say that your air intake is hurting you unless you are running near red line, same thing with your exaust, it might be to big and your tranny is hurting your highway mileage more then anything, for better city mileage shift earlier to keep your engine at lower revs.
I think blocking off your grill that is not in front of radiator would help, removing your fog lights would mostly help with weight savings, and your lower lip might even be helping.
also, check your tire presure, bumping it up to the max recomended psi might be recomended.

I added the fogs recently cause I am a JDM fanboy plus me and my friends all agree they help the look of the vehicle. They only add minimal weight. The intake I have was to replace the god awful jerry rigged cold air intake that was in it when I bought the car. The exhaust, well how does that hurt it when it is less restrictive?

This thing is my DD but it also my only car so I do power mods on it but I try not to screw with it too much cause premium ain't cheap. I'm waitin till I can get a more fuel efficient DD before I go all out on this thing (cam gears, CTR cams, higher compression pistons, AEM Hybrid Intake, injectors, maybe a turbo, etc.). I'm just tryin to see what hurts me real bad and what don't in MPG. I want my car too look and perform good while still maintaining decent fuel efficiency.

you can do some searches here on peoples opinions on exaust, and if you read up on exaust and intake design, most engeners seem to agree that an intake that is to large can be as harmfull as being to small, air is a fluid, and if it's moving, then it is best to keep it moving at a consistant speed, a larger exaust lets the exaust slow down to much, kind of like a dribble of water coming out of a sewer pipe, it isn't able to maintain momentum in a large pipe, same thing with the air intake, air intakes of course are much easier to swap out, so in theory you could have two, one for normal use, and one for when you want to impress people.