The answer is possibly in the question... If your alternator hasn't been charging sufficiently probably due to a faulty voltage regulator for a while, you have been driving along with just the battery charge voltage to keep the ECU and it's relevant input signals in constant contact and signal voltages. In particular the fly by wire throttle position circuit then it will be difficult for your ECU to ascertain it's position in relation to engine speed and road speed.
So initially you may have 14v+ charge rate and then below 12v as you continue on your journey thus intermittent signal loss as it fluctuates up and down.
If the alternator has been repaired or replaced and if the same issue is still there then the next logical step would be a possible loose multi plug connector between the throttle position sensor and the the throttle pedal itself. It's a common issue where over time the vibration can make the pins inside loose. It is usually a white plug located behind the glove box area but depending on what pedal assembly they used at the factory, it could be located closer to the pedal.
Just follow the wire from the pedal itself to where you find a plug connection. Clean the contacts and make sure they are tight and cable tie both sides of the plug together to prevent loss of communication in the future.
I'm pretty sure the alternator issue will be the underlying factor though, they tend to start giving non specific electrical signal issues for a while before it becomes obvious that it's an alternator fault itself.
Hope this helps mate, don't give up. Alternators are a wear an tear item that can last for many, many years without trouble... They all fail eventually on every single car no matter what make they are.... But as you can see, can cause a myriad of faults, particularly on an Alfa that relies heavily on a lot if electrical circuits.