occasionally bogs from full throttle


I have a 06 busa with 46k miles I've recently replaced the fuel pump and cleaned the injectors and recent plugs. sometimes when it warmed up it will bog down during acceleration as well as right after I let off it just won't give it any more other times it will hit 10k rpm and completely let off but it doesn't happen every time, the lights also have some sort of flicker, I've been told I could try to replace the rectifier the bike doesn't have any special lights or any electrical modification other than a PC5-V so I doubt an electrical issue
so I doubt an electrical issue

Start with a neutral approach and no guesses.

I will copy the data that you posted to the Showcase because it is valuable:

my recently bought 2006 Hayabusa has problems I don't know where to start. the bike has a pcV on it not sure what tune it has, it will occasionally die at random while really getting on it, it surges and bogs down as the headlight will go in and out, the previous owner told me it might need a fuel pump and dealership told me it needs to be tuned and to remove the power commander V. not sure if the headlight problem correlates with the fuel problem but anything helps

2006 hayabusa 46k miles
power commander V
ECU flashed

Do you have the service manual? If not, just ask as it is available as a download on this forum.

Are the new pump and injectors OEM or aftermarket? I know that members here allude to potential problems with aftermarket items.

The aftermarket fuel computers can fail. They are like a personal computer and are subject to destruction from the intense heat. You could disconnect the Power Commander at first to eliminate that as a problem. The ECU can adjust for most aftermarket exhausts unless there is something extreme on it or an open header.

Because you just got it you need to be thorough with tests and maintenance items. Use a multimeter to run the electrical tests listed in the manual on the stator and rectifier when cold and after thoroughly heating the bike. Check that the kickstand spring is stout and is not a-floppin' in the wind. Clean and test the safety switches such as the kickstand switch and the handlebar switches. These all corrode and begin to fail after 12-14 years of age so this bike is due if this was not performed by the previous owner. Electrical components can fail when hot but work fine when cold, as the heat increases the resistance in them. Clean and tighten the high power connections including the ground.
the injectors were just cleaned and the fuel pump is a quantum systems pump, I got the power commander unplugged and it brought very little throttle response or it surges at idle, plugged it back in, and that went away, I've checked the kickstand switch as well as clutch. High power connections? today I'm gonna start with testing the tps and rectifier
High power connections?

rectifier, starter, ground connections...

Regarding the idle surging, I wonder if the throttle body requires synching. Excess fuel, should that map indicate such, can tame this or cover it up by filling the problem lean cylinders.

and rectifier

Do not forget cold & hot impedance measurements of the stator coils and AC voltage output.
have not been able to get to testing anything yet but had a quick stupid thought i figured i should throw out there, the gas tank isnt sealed all the way, just noticed a gas smell whenever i get going and get down was thinking maybe a pressure problem maybe nothing
Okay just checking , tps is within range rectifier plug is questionable, very dirty inside and it looks as the bikes harness has melted at the larger red wire, yesterday while going up a hill at full throttle it just quit , once I pulled in the clutch it completely died , cycled the key and it started right back up , I tried to recreate the problem going way over the speed limit and it wouldn’t do it , ran great afterwards

Move the C-clip "down" two positions to fatten the transition range metering...

Update I had a injector rebuild kit decided to use it , installed correctly, reinstalled into bike and now it smokes like crazy , the old filters didn’t look to bad so I’m not sure what could cause it to smoke so bad after cleaning them
$200 later a shop told me it wasn’t a fuel problem and couldn’t figure it out awesome, found the tip over sensor full of glue and found a resistor in it, got a tip over sensor delete plug and it fixed it , wrong resistor, I wish people would just wait for the $20 part instead of trying to good time with it at home