I'm far from an expert, but the fuel injection is totally dependent on the throttle position sensor for metering fuel so if that's disconnected all bets are off. It's not a simple matter to reset the throttle position sensor either. (I'm only familiar with the EFI on my Duc but I think it's similar) It's an electronic calibration. You need software (Technoresearch ??) and a cable to connect to the ECU to make what minimal adjustments are available to you. You will also need a air fuel meter to know how your tweaks are affecting combustion.
IMO EFI is a PIA on a dirt bike. Actually I've more than once wished I had carbs on my Duc. It is not a shadetree mechanic type operation.
I'd say find a shop that can set the thing up correctly.
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Ross
'05 MC 250
'91 Husky 610wxe
'04 Duc M800 R.I.P
'06 Duc S2r 1000 R.I.P
'07 Duc S2r 1000 still rubber side down...
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