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ECU Flashing FAQ / General Info

Motorcycle ECU Flashing – What You Need to Know

What is ECU flashing and how does it benefit my motorcycle?

Flashing an ECU means rewriting the factory software inside your bike’s "Engine Control Unit. Unlike a piggyback tuner (which only tricks the ECU), an ECU flash makes direct changes to the fuel, ignition,, throttle parameters and other settings the bike actually runs on.

Why does this matter? From the factory, motorcycles are heavily restricted due to emissions and noise regulations. Manufacturers often limit throttle response, horsepower, top speed, fuel mapping, and even ignition timing to meet these rules. With ECU flashing, CJR is able to:

  • Unlock hidden performance

  • Improve reliability and throttle response and overall on/off throttle smoothness

  • Remove unnecessary restrictions

  • Optimize fueling & ignition for your setup

The result is a motorcycle that runs stronger, smoother, and cooler — exactly the way it should.

Which ECU flash is right for me?

Every rider’s needs are different. Using our Dynojet dyno and race-tested data, we create flashes suited for:

  • Daily riding on a completely stock or lightly modified bike

  • Fully built race machines with extensive modifications

Whether you want more horsepower, a smoother throttle, or just better overall reliability, we can recommend a flash or build configuration tailored to your riding style and budget.

Will flashing help a completely stock motorcycle?

Yes — even stock bikes see noticeable gains. Many run too lean from the factory, leaving performance (and reliability) on the table. After flashing:

  • A small bike like a CRF110 may see ~0.5hp (7% gain)

  • A liter bike like a CBR1000RR can pick up as much as ~20hp (15% gain)

After a stock flash, we generally have the next tune upgrade available, for a CRF110 for example - you can get double the power with our stage 1 hard parts/tune power package.

However, even if you haven’t added mods, flashing improves throttle response, heat management, and overall smoothness.

Is ECU flashing reliable?

Absolutely. In fact, it often makes bikes more reliable. Factory settings are tuned for emissions, not engine health — which means lean fueling and soft ignition tables. Our flashes optimize fueling and timing for safe, consistent operation.

As long as you:

  • Use the fuel type and injector we specify for your tune

  • Keep up with general maintenance

…your bike will be just as safe, and often more reliable, than stock.

What if I already have a Power Commander, Bazzaz, or another piggyback system?

You don’t have to get rid of it. A piggyback system can still be used alongside a CJR flash:

  • Leave ignition tables at zero to let the flash control ignition timing

  • Use the piggyback for accessories like quick-shifters, dataloggers, autotune for fuel, or map switching

  • Always confirm AFR before and after adding a piggyback, as they can sometimes alter fueling even when set to zero

Do I need a new tune if I change modifications?

It depends.

  • Small changes (like removing a backfire screen or exhaust baffle) often don’t require reflashing and can be safely used on the same tune. Some exhaust may have more or less restricted baffles than others, so it's always good to double check with your tuner. 

  • Big changes (engine work, new exhaust, intake mods, higher compression, injector, etc.) do require an updated flash

If you’ve been dyno-tuned locally, you can also send us the dyno file or datalog and we can update your ECU remotely.

What is your turnaround time?

We aim for 24–48 hours once we receive your ECU.

  • Same-day service is possible depending on mail arrival times
  • Expedited shipping is available on request
  • Orders generally ship the following business day.
    - UPS - Delivers/picks-up once a day around 10am-11am - USPS - Generally delivers at the end between 4-6pm - Fedex/DHL - Delivers Noon-4pm Orders with a mail-in ECU do not ship until we receive your ECU. Once your ECU arrives, we ship it back with the hard parts on a single outgoing shipment.

Additional FAQ -

Do I need to run different fuel after flashing?

We offer different tunes for different fuels, it is always best to get the fuel your bike is tuned for. Higher octane fuel is always safe to interchange on a lower octane tune - for example a tune for 91 or 93 octane, would be safe to run 100 octane, assuming it is not an oxygenated fuel. If tuned for 100 octane, it would not be safe to use 91/93 and risk fuel knock/detonation.

Will my bike still adjust for altitude and weather changes?

Yes. The bike still uses intake air temperature, O2 sensor(s) and manifold pressure sensors to automatically adjust fueling. We’ve tested this in extreme high/low + hot/cold conditions (including the Rocky Mountains and Apalachin Mountains, all the way down to sea level at Daytona) with excellent results and custom tune adjustments based on your elevation and weather conditions.One of the things we do differently than most tuners, is optimize the stock O2 system. This allows for a richer target AFR during the closed loop areas of the ECU. Leaving the O2 system on allows for subtle changes of bike to bike varience, and a good consistent idle + tip in throttle for various condition.

Do I need to remove my O2 sensor?

No, in fact we recommend keeping it installed. One of the things we do differently than most tuners, is optimize the stock O2 system and it's learning capabilities. This allows for a richer target AFR during the closed loop (autotune) areas of the ECU. Leaving the O2 system on allows for subtle changes of bike-to-bike variance which provides a good consistent idle and tip in throttle for various conditions.

Do I need to block off my PAIR system?

This is optional. If getting custom tuning done on the dyno, it is required to be blocked off. Generally having this in a stock setting will result in some additional crackle on decel. 

Will I get a Check Engine Light (CEL)?

Generally you will not get a CEL. Some models like the Honda Grom/Monkey for example, may see a temporay check engine light (steady light, not flashing) which is related to the ECU not seeing the evap system during the flash process. This will generally go away after a few rides, however any persistent CEL's would recommend to contact us to ensure it is not something else underlying. 

Do you offer “flame” or “pop/crackle” tunes?

Yes and No. We don't offer the overly loud pop/bang tune. This is caused by using a negative ignition timing on decel and with that we have seen too many cracked cylinder over the years directly related to the pop and bang tune.
We do offer a light decel "crackle tune" like what you may hear at the race track when bikes are under heavy braking areas. This crackle comes from a fuel overrun on decel, which does require to have the setting "Decel Fuel Cut" or DCFC turned off. This does require a full system catless exhaust to fully benefit the noise. 

What is the ECU Flashing Process, how do I send it in?

For the Mail-in Flash it will require you to mail in your ECU. Ensure your order number or name/info is with the ECU, so we know who it belongs to. Send you ECU to us via preferred shipping method (UPS, Fedex, USPS, DHL) to -

CJR Performance
5825 E Hwy 163
Columbia MO 65201

ECU flashing is turned around and shipped back within 1-2 business days. Please include a note with your ECU that has your name and order number on it. We do not send labels/boxes to ship in your ECU. The shipping paid at checkout covers us shipping the ECU back to you after we receive it. 

*If a mail-in ECU flash is purchased with other products, the other products will be shipped back in the same package the newly flashed ECU that is being mailed back to you.


Why Choose CJR?

At CJR, we specialize in Honda performance and ECU tuning. Every flash is:

  • Developed in-house on our Dynojet dyno
  • Tested and refined at the racetrack
  • Custom-mapped for your exact intake, throttle body, manifold, injector, camshaft, cylinder head, piston, and exhaust setup
  • We are located right next to our family Honda dealership, which allows quick access to parts, diagrams, service manuals, and general information
  • If we don't have an exact tune, often times we'll take one of our shops test bikes, build it to your required spec, tune the setup and then send it out your way. 
  • Backed by one of the largest tune databases for additional upgrades for future modifications

We’ve helped everyone from daily riders to pro racers get the most out of their motorcycles safely and reliably. If you have any questions or concerns, feel free to reach out and we would be happy to help!

 

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