Mario,
Make sure that whoever does the new distributer installation fully understands how to set-up a dual synch distributor. The distributor will offer both a cam and crank signal which are essential to full timing control and for sequential fuel injection...
Was there a cam signal to the ECU before (my guess is no...)? If that is the case, then your EFI was set-up in batch fire mode and not sequential mode.
I have a feeling that once everything is installed and configured correctly, it will be a different car.
Here is a video of installing a dual synch distributor for the Sniper EFI. Your process may have subtle differences but much will be the same.
Andrew