https://www.ebay.com/itm/KTM-690-DU...-2008-2009-2010-2011-75605083100/283212149836
$260 shipped but would do the job.
Here's the airbox:
https://www.ebay.com/itm/Airbox-Box-Air-Filter-KTM-Duke-690-R-2010-2011-Air-Filter/133320727794
Here's why I was a little side eye at the dyno tuner saying it was "good" with it mapped as is. Gonna go into a bit of depth here to try to communicate the detail - apologies if this is already stuff you know.
The two ECUs work together as a unit and you can pretty much treat them as one unit. I don't quite recall which one controls what for that gen of 690, but the throttle calibration and idle reset are basically things that should be done with an oil change just as a default to try and keep the bike tip top. Again, designed for race use, not really changed much from there before it was sold to consumers. These, along with the O2 sensors, perform fine tune adjustments that work within the parameters of what the ECU can do while still passing emissions. They can only really change fueling a little. Most bikes are tuned lean right up to the very edge of not running to pass emissions, which is why sometimes those resets can nudge the mixture just rich enough to stop lean stalls or flame outs.
The PC5 is a piggyback unit that intercepts the commands the ECU sends to the fuel injection (and spark, if they support timing), and changes them beyond the parameters the ECU would allow. If it doesn't have an autotune unit on it, it can't do live changes, and most don't adjust for different air temperatures. They also require you to disable the factory O2 sensors, or eventually the ECU will "learn" its way back to the emissions compliant mapping. However - the piggyback unit doesn't have any way of knowing what is actually happening with the motor. It just knows "if you're at x RPM with Y throttle, add or take away this much fuel". They all start with a zero map (no changes from what the ECU does normally), and then you either download a map and hope it works, or you ship it off to a dyno tuner to have the controlled conditions where you can fine tune each RPM and throttle opening and figure out if it needs to be richer or leaner.
Unfortunately - if some part was on its way out, or the bike is running poorly, you don't know if the A/F ratio is off because the factory ECU map isn't quite ideal or if it's because the part happens to be failing at that moment. In an ideal world, you should have a full tune up and valve check done, get the spark plugs changed, the air filter changed, oil, everything, then do the ECU resets, throttle calibration, and then you put it on the dyno and tune it. Then you know that the ECU base map is determining as much of the fueling as possible, and you should be confident that your changes in the piggyback unit will fine tune the base map, and not be trying to address some other problem. As spark plugs wear and the air filter clogs and the valves go out of spec, it'll start to run a little worse but it shouldn't be noticeably so, and then when you check the valves and do the plugs and filters it'll go back into being roughly ideal.
But given that the bike wasn't running properly and the dyno tuner reported it couldn't hold an A/F ratio, that should have been an immediate "stop the dyno tune, figure out the root cause of the A/F ratio bouncing", because the whole point of the piggyback unit is to let you get a specific A/F ratio. You can bandaid a, say, failing fuel pump by turning up the amount that the piggyback unit says it should inject (fuel pump puts out 20% less fuel than expected, piggyback unit says "inject 20% more fuel", and now it runs in the ballpark of okay) but as your fuel pump continues to fail, it will just go lean again. Given that fuel pumps don't usually fail all at once, but tend to perform worse when hot, or under certain conditions, there's no way to know if the dyno tune was when the fuel pump was operating properly or not. From what they said, it wasn't, so it would need to get re-done regardless. Assuming it originally had a map on it before they started tuning it, hopefully that map was kept and was done from an ideal state, so as long as the bike gets fixed, that map would be fine.
The other thing that makes me sigh about all of this is that you can actually just modify the maps in the stock ECU with the right cable and software. The earlier KTM ECUs weren't locked down super hard and you can just tune the ECUs themselves without worrying about all the complexity of a piggyback unit and the additional wiring. TuneECU is free! (but most dyno tuners don't know how to use it...) Also, if they tune it to the A/F ratios that a 600 would run, you're gonna end up with a grumpy, hot bike. These bikes like to run real rich.