There is always the potential for some sort of wiring fault when you do a big job like a transmission. Regardless of the specific location of a given component, you always run the risk of dislodging or breaking some wires or a connection. As unlikely as that sounds, it is still a possibility. You can't, in fact, alter the timing on that car.

A question I would offer is, did you remove the flywheel? If you did, did you put it back exactly where it was? Or did you dislodge, or somehow hit the crankshaft sensor on the flywheel, bellhousing, or otherwise, when you were moving things around? Additionally, is the wire to the crank sensor disturbed in any way?

The engine computer is NOT very effective at diagnosing bad crankshaft sensors. It tends to read any signal at all as "good" and no signal as "bad". There are in-betweens that exist with those sensors. It would be perhaps a good idea to change out the sensor and see if there is any difference . The reason I ask about the flywheel is that there is a specific indexing mark on the crank that the speed sensor has to see in order to determine timing. If it doesn't see it, it doesn't trigger the proper spark timing and thereafter it is a vicious circle of poor running and/or no running at all.

I suspect that the vacuum line to the flame trap blew itself open because of the crankcase pressure difference from normal (knocking or backfiring). I would also check ALL vacuum connections to the intake side of the engine. This all seems simple, but if it occurred at the same time as the trans swap, it is fairly likely that something is directly related to said exchange.
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1992 940 wagon, 77k
as well as others.