As said before, I would go for pump sync, could easily be 180 out, even though you have not had the pump gears out of mesh you have had the cam belt off, remove pump sensor and set engine at tdc with cam tools in place, you should see the lump on the pump gear, if not cambelt off and turn crank one turn.
Another problem to add to the other suggestions (not likly to stop it starting) is coolant sensor wiring breaks, causes dash lights and head lights (you would swear it to be an alternator fault)to flicker at idle and cure as soon as the throttle is touched. All this and not allways DTCs, Best look in live data at just coolant temp.
One other thing primary pump should run with ignition on for about 10 secs.