Hi OP, congrats on the new bike and hello from a new poster (hi).
I have had a K3 DL1000 as a daily ride since 2006 and have been battling with popping and rough running especially at 3k to 3.5k area for years. I built a "Teka" box but adjusting the ECU did not solve the issue and just lead to higher than desired fuel consumption. Like all the DL1000s it seems the warmer the weather the worse it ran. This is what I have done to solve the issue:
1. Sharealike clutch basket mod (which you already have)
2. Balance throttle bodies (this also ensures the inlet boots are fitted correctly)
3. Check the vacuum hose that runs from cylinder 1 inlet to a vacuum reservoir and further on to the MAP sensor fitted at the rear RHS corner of the airbox. Mine had begun to split at the inside layer so was leaking and lead to bad throttle response.
4. Adjust the TPS to go from '_' to '-' at around 1400 rpm (TPS sync procedure is in the service manual).
5. Disable O2 sensor by cutting one of the wires in the ECU loom.
6. Finally to battle the bad running in traffic/hot weather I moved the inlet air temperature sensor to the front of the airbox. The stock location at the rear bottom corner of of the airbox leads to the sensor heating up when stationary and the bike then begins to surge especially on a hot day. I blocked the stock location using suitable bolt/nut/washers/o-rings combo. I drilled a new 12 mm hole on the front wall of the airbox just underneath the air filter element and screwed in the sensor with some sealer. Not sure what the thread of the sensor is but a nut with correct thread would be nice to have to secure the sensor in place but so far so good without it. To extend wiring to the new location the connector needs to be cut off and a length of suitable wire soldered on.
I think first time ever since owning the bike mine runs like it should with no roughness. The jury is still out regarding the fuel consumption but 1st time in years I'm totally happy with my DL. In the past three years I have been averaging 49 MPG according to fuelly but the fuel mixture has been a tad too lean.
PS. I also fitted TRE box with 5th gear mapping to mask a problem with intermittent gear sensor that lead to O/D light coming on on 3rd gear and the engine management switching between the maps causing surging. This gave the bike a better throttle response at lower gears in the expense of slighty more jerky progress in town. But it is totally manageable. You can feel the secondaries immediately open fully each time the throttle is applied. You'll soon get used to it.