Look at the subthrottle as a light switch. More like a rheostat room light switch. You have the main throttle at the cable being a normal on/off light switch. No matter how fast you flip the on/off switch, the rheostat [subthrottle] will rise as in a smooth linear feel, like the room goes from dim to bright with a twist of the rheostat switch.
All that sub is doing is slowing down the air going in. If you remove the flies, you increase the speed is all that occurred. You changed nothing to the fuel trim being the crank and your throttle pulse at the vacuum suck off a sensor is one feed to the fuel trim. That cable yank just told the ECU the throttle moved. Then there is the throttle sensor that moved too is keyed to the main throttle cable. So, you have all this input and that throttle apply you make is to cause/effect a smooth transition of air speed to slow down, give the bike a more linear glide rather than all this abrupt torque that now takes off at a much quicker speed... Being you just caused the air to move without a restriction in the way.
What happens when the subs are removed and the air is sent in quicker? Right off, someone thinks, "Lean?" In the factory service manual, someone just disputed a lean condition as in: "The bike is designed to work if the sub system fails.' 'We open the subs and now where is the lean if we open the subs in the practical move?" Basically, that is what the book states and then asks the question when someone shouts, "LEAN."
If the subthrottle is tied into the gear position sensor, the wire nicks to ground or is unplugged, the ECU simply sets the subs open. This is a pre-designed backup to fuel injection. If those subs ever fail and close like your main plate is now; how will you pull air in with that sub closing the door on the air? YOu would stall if that sub did not open> The more you try to suck more air is more cable pulling about to kill the engine. So, the design is for the subthrottles to ratchet open rather than close on a backup or sensor failure.
So now you have to ask yourself it the design codes to open the flies, the book states it is safe to ride.... Where in the book did it say it was dangerous to ride it? The factory knows it is not going to lean is burn down a piston? Safe to ride means WOT the throttle does it not? If that fail-safe/backup was not safe like redundant, where does the lean come in if Kawi [and add the rest of the fail-safe bikes which also] have the same theory covered is think about air speed and what do you need to be in a dangerous lean?
Did I not have the same redundant gas mileage hacked or stock? Yes, I do have the same mileage either stock or in, redundancy. No, there is no lean the bike cannot handle. I am open sub without piggy. I am 4-in-1 is open pipe is without piggy. Air cleaners with or without is a slight bog but now how can NASCAR toss in a restrictor plate and does the engine lean out or does the same engine run out of air at higher rpm is no lean, just a door restricting the same air as the subthrottle. Only the sub moves if you catch how many steps keep falling back to air speed and a restrictor plate.
There are few ways to remove the subthrottle plate or the complete sub system itself. If we are on a scale from 1 to 5, five being the most difficult, here are a few ways to achieve faster air speed and how easy or difficult the job can be:
1. Screw Removal. This is the most common way to keep the bike from coding and losing your display on the dash. Difficulty in execution is a, "2" category. The sub-shaft can move and cause the screwdriver tip to climb out and strip the head. You must have mechanical skills for this, plus a good selection of tools to begin with. If you do not feel confident with the mod, there are a few ways that will work just as well without an array of tools.
2. GPS Code Triggering. There are plug-in devices out in the aftermarket, or you can set the code by using a resistor. The resistor is used so as not to short to ground and blow a fuse, nor is this to set the other code being the GPS is tied into a few other sensors as a group to cause/effect a code to safely backup itself. Difficulty to set the subs to open is category "1" in execution. This will cause your gear select window to show a number (6) in the window. If there is a swap in wires to trigger, then the next code will set in the dash, showing you there is a problem with said sensor. This is normal and what you did was code to the redundancy. No harm, no foul you might say.
3. Remove Subthrottes/shaft/hanging hardware. This is probably the most difficult to disassemble and reassemble, so lets call this a "4" as in difficulty to execute. This sub-gutting is more extreme and will flow the best. There are less parts in the way to restrict the air from flowing. The shaft is one more part in the way of filling the cylinder as soon as possible. Notice that air fills that shaft space. That is that much faster that space the shaft took up is that much faster the air is without the shaft in the way.
4. Subthrottle Shaft Locking. Difficulty to execute is rated a "1." This is the least intrusive of all the sub plays you can make. This is where you remove the choke system that the subthrottle uses for it's cold choking. This opens the main throttle a little so there is a rich fuel set to start on cold engines. By removing the tiny 'E-clip," you can pull the choke assembly off, then ratchet the subshaft open. You will have to remove the subshaft's actuator or else when you turn the key on, the gears inside will strip being the shaft cannot set itself open for choke or running function. You do not want that; being you would have to buy the whole throttle body unit. The actuator is not rebuild-able. You would now have to make the shaft stay open somehow.
This is the least difficult and the quickest way to return back to stock. Yes, you will lose your dash display.*
Note: When setting any other sub mod than removing the screws from the flies, there is no code set on the dash, nor do you need to increase the fuel as in installing a PC to re-trim for a lean condition. The factory has you covered either way. You have to understand air speed and what you just did so you understand you changed the air going in. The telemetry knows where/how to trim the fuel being you removed the restrictor plate. Did you lean out the air or did you let more air in is there is so much air the cylinder ingests and that was the same air with the subs only it moved a little quicker in. Where is the lean?
Here is #4 Sub-mod: 
