Captain Proton

Time will tell, but Im not convinced that would have been your problem.  
There are 2 TP sensors connected to the same butterfly shaft, so yes - if there was dirt of something stopping the blade from closing then they would read higher than normal when closed - but since they are both connected to the same shaft they would both read higher by the same amount.  
The fault code you had was due to the sensors reading differently from each other.  One was showing 3% more than the other.  When the sensors read different the ecu has no way of knowing which one is correct.  

The 2500rpm with pops and bangs is the throttle system going into safety mode, if it thinks there is a safety issue it shuts off power to the E-throttle (the spring will slightly open it to about 7% throttle) and a rev limit of 1800rpm is activated.  
Can you attach the tune and a short log of some pedal presses before cranking, then capture a crank/start up as well.  It would be nice to capture the fault happening in a log if you can but otherwise just a log of a start up may be enough to see if it is getting close to the error triggers.

Anything above 150Hz means contaminated fuel.  Most likely water but could also be diesel or similar.  You will have to drain the tank

Are you getting fuel flow and pressure?
Any idea the condition of your fuel filter.

It sounds like the ethanol sensor digital input is outside of its operating range and has switched over to the fault/error value.  The fault setting is user adjustable but most commonly it is set to zero% so that it if it fails it runs like crap and you know there is a problem.
The normal operating range of a flex fuel sensor output is between 50 and 150Hz, the ECU will consider it in error if the frequency goes below 40Hz or above 160Hz. 
So to get yourself running again you can temporarily set the fault setting to say 85% (or whatever you believe the E% in the tank is at).  I would only drive it easy like this though and set it back to zero once fixed.
Here's where you find that setting:

 
Now, to check what is causing the problem, with the engine running you can go to the runtimes screen (F12), digital tab, and find the DI that is set to ethanol sensor (in my example below it is DI5), then look at the DI frequency reported on the lefthand side (mine is showing 120.1Hz).  If it is showing 0.0% then there is a wiring problem - a loose connection or no power at the sensor or similar.  If it is showing a frequency but it is below 50Hz or above 150Hz then it is a fuel contamination problem - most likely water or diesel in the fuel.