Problem remains...
 

Ok, so I'm bringing up this issue again since it was not resolved. The bike seems to run rough sporadically. Not all the time. Lately it seems to run well except at really low throttle. So if I'm cruising at 70 its fine, but when I see a cop and slow down (not shut the throttle completely) it runs really rough. This problem started suddenly while riding, so it is not something I tuned, like a jet or something. It ran fine, then one day while riding just started running crappy. The timing is perfect at idle. I unplugged, cleaned and reconnected my electronics about a million times. Checked my grounds. Went through the carbs several times. I am so frustrated... I have no idea what it is... Any suggestions? Oh and I replaced the plugs and plug wires, and the shitty wiring the last guy did to the coils. ideas?

if your pilot jets are still stock, and you have a pipe and other stuff like maybe filter mods, it would be too lean at partial throttle maybe ( dont know your altitude)
But if some bozo had his hands in there rejetting, and screwed up on the choice of needles or mains, you could have other issues.

My main question would be ,
have you actually had the carbs cleaned by a professional shop or maybe done a complete disassembly yourself to verify the carbs are even clean ?

People, running some crap in your fuel IS NOT going to suffice as any sort of real carb cleaning.
If someone tells you it is, that individual who told you that is a moron.

SeaFoam works great. It wouldn't work for chunks of dirt or debris though.

Yes I have done a very thorough and complete cleaning. all jets are clean, float valve looks fine, as you know the float height is not adjustable, everything looks fine. And like I said, it ran fine, then suddenly something went wrong. And my pilot jets didn't exactly change size mid ride... so I don't think it has to do with anything carb setting like that.

chunks ... those intrusive little bastages that love to cling to the insides of your jets ... gleefully changing the jet size to random sizes ... automatically !

true, but I've had the carbs apart at least 5 times since then, and they are spotless.

But yes indeedy ...
Jet sizes do indeed change on their own ( when carbs dirty )
But if you say its clean, lets assume it is.
In this case ... you have an issue that most likely will require examination
at someones shop.
A lot of easy to diagnose stuff in person, is next to impossible to locate from a remote location on the internet.
A mechanic hearing and feeling what a bike does in person is 50 times as effective than over a phone.
I bet its something like a random air leak into the intake or something lame like that.
have you checked for air leaks yet?
Several techniques, my fav is ether.
but keep all flamable stuff away from people who would hurt themselves with it, of course . :D

it's worth mentioning that I'm two classes away from my degree in automotive technology, so I know my way around an engine... And this is not my first bike... I've had to tune plenty of carbs before. Not that I'm above missing something obvious, clearly I want some help, but I'm just saying I'm not completely retarded.

Thats good, you have things in your favor.
Some , well they just dont have it yet.
Air leaks are motherfuckers, and can cost you an engine.
I would check for them if you havent yet.

And, a lot of auto-tech completely does not apply to Japaneese motorcycles.
Its a completely different book in many aspects.
It sure helps though.

Okay then, use the choke as a diagnostic tool. Pull it out a little while riding and see if it gets better. If so then you're running lean. This could be your mixture screws or a clogged idle jet. Also, spray out the holes in the carb throats with a good carb cleaner - yes, the little ones on each side of the throttle plate. Cycle/remove the mixture screws and set them to 2.25 turns out. Follow all that up with a carb sync and that should solve your problem.

and while you're in there, set you TPS to 450-500ohms unless you've already adjusted it.

Check the vacuum line
 

One possible cause, I think, would be a cracked or rotted vacuum line. Remove it from the nipples and inspect the ends for wear or a loose fit. Trim or replace as needed.

If the choke is not doing much better of worse, I'll check those valves clearances, they can make the low end go real bad, or a compression test idf you have access to a meter

Alright guys, a little update here. Last night I changed the orientation of the back of the petcock. It was facing left, now it's facing right. Anyway I was thinking that maybe the vacuum line (because it had to make a sharp turn) was kinking. Well After I replaced the line (which was a clear plastic aquarium tube lol) I took it for a test drive and it ran perfectly! no problems at all! Also, I let it sit overnight with the fuel on, and it didn't flood! for the first time since I got it! You guys are geniuses. Thanks for the insight! I think I have a fully functioning hawk now! Whoo!

but if you were still clinging to that speed freak Ho-Bag and letting her rule your mind, your hawk would probably still be in disrepair.
good you are moving forward!

It's always the little things.

wow!that's great news. What a pain in the ass for such a stupid little thing like a kink in a vacuum line. Like a great motorcycle mechanic used to tell me often, "Attention to detail". Now you can out there and ride that bitch like it's meant to be ridden, huh.:congrats: