how much of the other stuff was done at the same time as the problem appeared? for example, if the coils were removed, are the connections back in the right place? (e.g. for a 1989, the plug with the two red wires should be on the 1-4 bank coil, the one with the red and white wires on the 5-8 coil. it doesn't really matter which module the big connector is plugged into...you can swap the connectors between modules for testing, but you can't swap the red-red and red-white plugs between coils without moving the secondary wire also). the comment about checking the sensor and coil harness plugs is also a good one, since those are disconnected when the oil cooler air scoop is removed. It's best to check the various resistances and continuity from the ecu connector, which then covers those connections as well. the flywheel mounting holes are slightly asymetric...someone would have to be quite forceful to mis-orient the flywheel. I don't recall if the pegs in the flywheel that the sensors are detecting can be taken out and put back in wrong spots, and unfortunately can't find a picture of a 328 flywheel that would show the correct peg orientation wrt the tdc marks, but it seems that if the flywheel/pegs were somehow off, the engine wouldn't really run at all.
Update on this problem: the flywheel is in fact out of place. The PM mark is aligned for cylinder nº 8, not 1 !!!! Well, it is number 1 on the other bank :-| Has anyone ever seen this mistake before ??