After perusing the forum for the past month or two, I did some research, bought the parts and modified a couple things all at once on the bike. First the R/R relocate and replace. Then I coastered it and completely removed the emissions component/hoses. Last, I did the ear shave, which meant re-jetting the carb. Currently running 142's/42's and 2 shims on the needle.

It's running and rideable again now, and I definitely notice a difference when it's WOT. it's got decent power at low rpms too, but when I'm doing 3-5k RPM the bike will bog down some, and i can feel it "pulling" intermittently. I've been experimenting with the Air mixture screws, too far in makes it worse. Right now they're like 3 turns or more out, almost to the point of falling out; and I'm still getting the bog.
I'm afraid to go out anymore, and am running out of options. Ideas?

What do your plugs look like? That is what I would look at before adjust the screws a bunch.

Try with the screws at 1 1/2 out, and move from there. You could be running really rich. Make sure your carbs are seated properly.

I'm curious about the plug's condition, though.

I can check 3 of the plugs... one I stripped and decided to just leave it in and deal with it later. Heli-coils don't look fun. Last time I looked at the plugs, a month ago, I cleaned the tips off, and they looked good I know they are decently new. I don't know gap sizes though...

By seated properly, you mean the rubber connections from the cylinder to the carb? If so, I had trouble getting those to align and cover both carbs entirely, but I do believe they are on enough to seal...

I need to ask, what air filter did you use?

Only the best, K&N RC-2340's

How about the air hose that goes to the right ear. Have you tucked it under the feul tank away from direct air flow?

Are you talking about the hose that goes in to the front of the front cylinder head? This pic shows the crankcase filter that I attached to that part.
Or the one that was apart of the emissions system that I removed?

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No. It is the one that comes off of the carbs. It has a "T" and it comes off of both carbs.

I don't know what you're talking about, and just examined the bike and can't find anything like that..

there are two hoses that connect to the top of the float chamber on the carbs they tee into each other and the one hose coming off of the tee is usually tucked into the right ear but since you have shaved those puppys off you need to tuck it back under the tank out of direct air flow or the wind whipping across it will cause the slugging you describe
at idle you dont feel it cause there is little wind and at WOT you are pouring in enough fuel to not notice it

its the hoses that come off these things at the ends of my fingers