2004 gen 1 power commander problems


I own a 2004 gen 1 that has been giving me issues for the past few months and i have found no answers anywhere. My mechanic doesn’t know what the problem is either.

I had a problem with a pwer commander 3 where i would be riding perfectly normal and would be able to get on it without any problems, and very randomely, with no real known reason, it would start to stutter and seem as if the fuel pump was failing. After a bit of maintence and a new power commander 5 everything seems to have gone back to normal, or so i thought.
The exact same problem has occurred again with the new power commander and i am lost for words. It almost seems as if the fuel pump is failing and starts to stutter the whole bike, but it never gives us error codes and we can’t recreate the problem on purpose. The things we have done to the bike are; clean/flush fuel pump
Make sure kickstand isn’t causing problems
Check wiriing throughout bike for loose wires
Tighten down all the wires on the battery
Purchased a new fuel pump
Tested the power commander 5 on 3 other 2004-2005 gen 1 busa’s (they all performed amazingly)
Replaced fuel pump relay
And there may be other things but i don’t know what they are.

The main thing that confuses me is that it runs perfectly fine without the power commander. No stutters, no random shut offs, just doesn’t have a tune on it.
The person who did the pc5 tune does it for a living and we tried multituple different maps and the problem still occured.

If anyone has suggestions, please let me know, we’re willing to take any help at this point.
I'll try that out when i bring my bike up to my mechanics tomorrow. About how long do you think i should test it or is it something that will show instantly. The stuttering is something that could take 2 minutes or 15 minutes to start.
Just contacted my mechanic and he informed me that he has checked the voltage multiple times and it has been up to standards and when idle and revving it shouldn't be causing problems. I don't think that the problem is the battery not performing.
I had a similar issue on my bike but it was only while riding when I got on it hard. It was the tip over sensor beginning to take a crap in my case. Unfortunately doesn’t sound like it is the case for you.
What I can say is the PC is what is driving your fuel. No PC no fuel.
What you have to remember is the PC is drawing a little more voltage than the bike normally would without it. Quick and easy first thing I would try is replace your “fuel” fuse in the fuse block (I’ll check what it is labeled tomorrow)
I have seen issues like these on customers vehicles where fuses have hairline cracks in the bridge and when a little more voltage is demanded they stutter.
Next thing I would do if I were in your shoes, rig up a relay to test. Give your PC clean and direct power from the battery. Basically what you would do is use a key on signal as the trigger, supply direct power and ground from the battery and put your relay “energized out” (87) to the positive input of the PC.
It definitely sounds like your losing voltage...maybe not in the bike itself but somewhere between the PC and the bike electrics.
It'll show immediately. As soon as you twist the throttle the voltage should start climbing. Is the PC grounded properly? I'll bet money it's an electrical issue. As mentioned above, the PC isn't getting clean power.
is this a Suzuki mechanic? like a dealer? because if not u might be chasing ure tail and throwing money away …. u cant just plug parts into a bike.,
He’s an incredible hayabusa mechanic who’s very well known in the southeast of the US. I’m bringing the bike in tomorrow to go over some stuff with him and we’ll check it out. I’ll keep this thread updated. Thank you all for the assistance.
So we check all the fuses, replaced one that was questionable, checked all the connections between the fuel pump and the main wiring harness and also just did a general checkup on all things. Plugged in the PC5 for the first time in about 3 months. So far i've put over 50 miles on it and i haven't had an issue with any stutters or anything similar to what i was experiencing before. I don't know if the single fuse replacement made a difference or not. My mechanic said it more than likely wasn't that, but, electronics can be temperamental. At this point in time, everything seems to be running fine and i finally have a tune on my bike again, which is great. If anything more happens in the future, i will more than likely return. Thank you to the ones here who gave suggestions.