Hi,
I'm not experienced with that year, but my limited experience and knowledge of engines leads me to believe you problem couldbe related to a spent Cam.
Figure this logic:
What does a Cam do? It times/controls the lifting of the fuel & air valve ports.
A great example of an 'overhead cam' is here:
http://auto.howstuffworks.com/engine3.htm
So, if the "orbs" on your overhead cam are worn down, or springs under the "rocker arms" that contol the valves are weak, then that could mean your backfiring (actually is) being 1 or more valves being stuck-open during combustion.
My feeling and knowing that Linc/Merc service departments aren't know to be sharp, especially with 10+ year old cars, they could've been offering a low-cost temporary solution to a minor cam replacement ($75 for cam, 2-3 hours labor @$85/hour).
The fuel regulator on EFI or SEFI engines just regulate the vacuum for sucking the fuel to the injectors.
The MAP sensor (mass airflow) is used to calculate the fuel/air mixture, and power-curve.
This is not a fuel problem.
Since the distributer is gone, and it's distributor-less, it would be a computer timing thing (a worst case scenario).
For 100,000+ miles on a SOHC (single overhead cam) engine, it probably worn cam and springs.
Was this car driven hard?
Later,