I have little confidence in aftermarket "tunes" doing what they claim and operating correctly.
If your O2 sensor ports are plugged then the first thing I'd do is re-install the O2 sensors and plug them into the ECU as originally designed.
If you have a way of re-flashing back to stock programming temporarily, do that ... even stock programming that doesn't account for your aftermarket exhaust. The aftermarket exhaust shouldn't affect part throttle operation much.
I find it rather unlikely that it only uses the O2 sensor readings at idle. On a late model bike with a catalyst (as originally equipped), it's more usual to operate in closed-loop (with lambda-sensor feedback) after cold-start warm-up, everywhere below a certain throttle position and below a certain RPM, sufficient to do the entire EPA or Euro 4 / 5 test procedure with it in closed-loop, for maximum catalyst efficiency.
My race bike has a reflashed ECU supplied by a well-regarded tuner for that model. My bike won't run acceptably without my own PowerCommander map superimposed. (Way, way too rich at part load - so rich that when coming down off of higher revs in neutral, it simply drops all the way to zero and stalls, without even trying to pick up a nice smooth idle. My PowerCommander map is full of negative numbers in the whole part-throttle regime. In fairness, the cam timing isn't stock, but the difference from stock shouldn't have affected it that much.)
I just got TuneECU to run on a Tablet I picked up today. I will try getting it connected to the bike and reinstall the O2 sensors, restore the air filter to the original cover as opposed to the bellmouth, and try running the
OEM Triumph Supplied Arrow tune to see how it runs.
From what I've read, the O2 runs
closed loop under 6% throttle (apologies - I said open loop in my first post because that logically made sense to me, but apparently when it collects outside data its actually a closed loop... confusing semantics
). People generally seem to say that this closed loop operation makes for very snatchy throttle at city speeds - hence going for O2 delete, and aftermarket tunes. One way to find out though!
I've poken to Champion a while ago as well about getting a personalized tune. They insisted on a Power Commander, though I really don't want to piggy back stuff and add more electronics. I remember them saying that if I could get TuneECU to run on a device and connect to my bike, that they could do a tune with that. I may go that route - but I am scared to know what it would cost me...
Ultimately, squeezing every ounce of performance isn't what I'm after. I just want it to run well, and for the engine to live a long and happy life.
Edit: I also know that my aftermarket tune has ignition advancing. I assume that is tied to the Map(?), and that when I switch to another tune, it will pull back the ignition timing to stock too?