The modern fuel injected system is far superior. I am a fan of tried trued systems like the Honda PGFI system. This was perfected on the track in the 80's then put into production. When I see all the struggles with KTM, #1 I am disappointed as I would love a reliable FI dualsport and #2 there is a lack of quality training and programs for technicians in today's apprenticeship system that usually means there is a lack of expertise in dealing with these systems at the dealer level when problems arise. I know I am up to my neck in this issue.
Businesses are leery of spending money on the training of mechanics as they tend to take the training and then leave their employer to chase dollars or start their own shop. The opposite was true during my three apprenticeships. So if one is to buy a problematic complex bike one needs to confirm there will be someone who is trained and experienced to keep the machine in service and on the road.
There are a few good guys around but they as I have stated before are far smarter than me and tend to stay out of these forums where it is very easy to upset people and alienate potential customers.
Any back yard KTM owner who wishes to conduct maintenance/rpairs should not forget the basics as well as the new tools of the trade which I find not many know how to properly employ in diagnostics.
I rode 15000 km on the CB500X and it did not skip a beat so there are motorcycles with good solid systems and when I find one that matches the KLR reliability/off road capability I will buy it. I am not technologically averse and as stated previously every morning I put on coveralls and pick up work orders that state all kinds of maladies so when I come home I really do not want to have to fuss with problematic "garage queens"
My guess is fuel starvation - I have a 2012, this summer got stranded in 70 mile due to clogged fuel pick-up strainer. I cleaned pic-up, replaced/relocated the fuel filter to outside the tank, replaced fuel pump w CA cycleworks pump. Bike ran fine for a week then had same starvation issues again - now it was the tiny top hat filter in the injector now that was clogged. I chucked top hat filter in garbage and back pressure cleaned out the injector (as per RTW Noahs youtube video via ADVrider) and has been running like a champ ever since. I also have order a tea bag filter from Pro-fil in Aus to replace pick up strainer.
I have never used a oscilloscope to troubleshoot a fuel pump. How will a electrically sound pump with mechanical issues (worn impellers, weak relief, clogged suction screen etc?) show a different wave form? This is what I was thinking with the amp draw question.
Could it be the that the THAD and APAD reference values given for the 690R in post KTM 690 EFI 2008 - 2013 : Idiots Guide are incorrect? Even the 08-10 690E values given there are inconsistent with the 2009 repair manual, which seems to state same values for all 2009 690s models (E & R):
1: Throttle Position Sensor closed: 0.5-0.54V
2: TPS open: 0.7-0.74V
3: Throttle Grip Sensor OPEN: 0.7-0.74V
There is no mention of closing the butterfly valve manually for the TGS reading, as specified "Throttle grip sensor CLOSED 0.70-0.74v APAD" in the Idiots Guide. This would explain your error codes and poor running engine, as sensor readings are outside of ECU expected ranges.
That being said, I am facing similar issues and have not managed to sort them yet...
If you fixed the issue, I'd be curious about the solution since it seems we have taken the same troubleshooting steps this far.