I have been having issues lately with my bike not running smooth, feeling jerky at cruising speed, down on power. The mods were a full TI-force exhaust, BMC filter, Ivan Performance TRE-8, PCIII. I removed the TRE-8 which made no difference. I removed the PCIII and now it seems to idle normal and revs smoothly. Before it would die out on the decel after reving. It used to run good with the PCIII but not so good the past year. Would it be ok to drive the bike for testing without the power commander with the full exhaust and BMC filter? I want to make sure the PC was the issue and if it is I am going to do a stand alone CBlast ECU flash instead.

"Would it be ok to drive the bike for testing without...?"

Yes. Beat crap out of it no problem. Then, check and clean air cleaner. Change plugs. Reinstall the pc and see if it runs better as before.

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I don't beat on my bike at all but I drive it enough to tell when something has changed power wise. Filter cleaned, new plugs before the PC removed. Same issue. If removing the PC would not have helped then I would be checking fuel pressure, pump, injectors, coils and looking at all the wiring harnesses and connectors. Is it possible for a PC to lose the throttle position calibration due to power glitch. I have seen some crazy stuff being an electronics tech on industrial machines, especially with wires partially grounding bringing the dc control voltage down enough to make digital controls do some crazy things.
I was not sure how lean the bike would be with full exhaust, filter and no PCIII? I don't want to put an bowling ball in front of the cue ball by flashing the ECU if I haven't found the root cause of the original drivability issue. I think the PC is that root cause but I need some saddle time without it to verify.

I don't beat on my bike at all but I drive it enough to tell when something has changed power wise.

That was more like saying, 'the occasional blip of the throttle never reaching reline will not cause problems like heat/lean/hurt the engine/etc.,' without getting into a long winded explanation about fi and carb differences.

Filter cleaned

Lets be real specific on this one. Tap the filter element on the ground and note debris. If packed with crap and the pile begins to mount = REPLACE! Let's be exact as in follow the book. We do not tap and clean/air blow gun a filter element. We tap and test for clog, replace at said mileage interval or sooner. Question: Do you have a filter past the mileage interval, yes or no? Yes... Then replace no questions asked or chase your tail. Suggestion at the end of this post is another test.

new plugs before the PC removed. Same issue.

Good call. That's how to eliminate symptoms.

If removing the PC would not have helped then I would be checking

1. fuel pressure: Where it would fall on its face, not keep running higher in rpm, go past this glitch.
2. pump: would be hard starting, poor idle, a drop in power when a certain rpm is reached.
3. injectors: if clogged, would cause that one pipe to be cool, has a self check code it can pop.
4. coils: again, it self codes, the header pipe is going to stay cool, be it spark or fuel if it is this.
5. wiring harnesses and connectors: for sure will spit codes if wires are out of the loop.

Is it possible for a PC to lose the throttle position calibration due to power glitch.

I'll say no at this point. Look at this area as if a radio station. The radio is set in RAM and does not drop this station out of the program. I doubt the tps to calibration will be out of sync once programmed initially. Cells do not drop out, think, once you program the RAM (your favorite radio station, etc).

I have seen some crazy stuff being an electronics tech on industrial machines, especially with wires partially grounding bringing the dc control voltage down enough to make digital controls do some crazy things.

Right, and when this wire sends itself to ground, someone in the ping is going to pop a code. No codes, no problem, all pings in balance meaning... in theory.

I was not sure how lean the bike would be with full exhaust, filter and no PCIII?

This is where the intake vacuum dictates lean/rich. You should know the motherboard is locked in the timing of the handcuffing there of; times millions of times it dumps data to retrieve new data and where is that tps positioned is way ahead of you in the calc and vac loads. This is no longer a fuel leaving a tube out of a carb. The vac dictates the tube is now a sensor... Big/Huge/difference are these two animals an how they feed.

I don't want to put an bowling ball in front of the cue ball by flashing the ECU if I haven't found the root cause of the original drivability issue.

You mean flash a bad ECU is a good call on your thinking this out.

I think the PC is that root cause but I need some saddle time without it to verify.

I'd have to agree. This bike sure codes when a system is on the blink. So as you begin to find out you take the basic theory, 'for every A there is a ping back to C, be it in DC or AC = For every ping, there is an equal and opposite out of spec here comes the code... Or your job-site, look at the new resistance ping to ground is out of spec and here are the needle readings to show a ping is going to spike 'hi' if the code is 'lo' and spike 'lo' if the ping is 'hi.' So it flip-flops, turns the code light on, timed to a timer and there is the blinking dash with a code in play.

Look at the pc and how it is hooked up to an 'output' signal. That pc is wired to the crank sensor/injectors/done. So if an injector failed, up goes the code and that plug's cylinder number. If it was the crank sensor, this has no backup and would kill the bike as in 'no start.' You hook up a water temp or vac signal, you cannot alter the water temp. That is wired up as if it was a temp gauge off the sensor, tied to the ECU remember, and no code pop occurs with the pc in play.

We would assume the conclusion is;
1. No codes present.
2. Run the bike without the air cleaner (mileage history and conditions) means you live on a dirt road is the assumption. So question the cleaner and run without. You don't beat the bike to hurt it in this test, because you're more feeding throttle in the linear opening, where this is going to clear or climb/fall/remain the same in the test of the driveability test.
3. The fuel pump is; do we hit redline? Then no, not the fueling feed if it hits redline. If it remains flat on it's face, no more rpm can it climb is stuck at this 3k area... then yes, sounds like a fuel pump.

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Thank you for the info. Very little dirt to none was in the filter, just a few bugs. It was replaced with the plugs and I rechecked it again before pulling the PC. I am going to take it out for a spin today to see how it rides. Just sitting in the shop it sounds much smoother without the PC and had no hard starts. To be honest it could have been the ground. It was installed at the water tank bolt instead of back to the battery grounding point. All the mods were on the bike when I bought it so I don't have a lot of info on the tuning. I assume they just used a Ti-force map from dynojet. That is a big reason I want to start over with the ECU so I know exactly the details on the modifications.

It may not be down on power. I just bought a 2014 Ninja 1000 today and it feels like a moped compared to the ZX14. I may just have gotten used to it. The only reel issue then would be the occasional hard start and low RPM stutter with it seeming like it floods out on aggressive high rpm accelleration. I will put the fairings back on tonight and hopefully ride it to see how it is without the PC. Need some exhaust and a flash for the Ninja 1000 now. Sure don't feel like a 140hp bike.