Hi Charles.
Auto or manual, first i would remove the synergy 2, then leave the MAF sensor unplugged see if it make any difference. If not try and get a T4 session on it, you could also do a leak back test, as the plenums been checked as the ECU got wet do you know.
Do you have UBP i doubt it though as you have a 2005, i have seen them with UBP if so put the hose into a bottle, and get someone to turn key to II is fuel flowing freely with out spluttering.
https://youtu.be/MikZPHxCUww