I've read all the posts so far and this certainly is a strange problem for a Contour V6. Definitely look into problems related to timing and the ignition system.
There is one remote possibility that nobody else has mentioned. The loss of power + popping in the intake manifold sounds like the old classic worn-out camshaft lobe problem that Chevy V8's suffered from in the 1970's and 80's. Chevrolet was too cheap to invest in proper heat treating/surface hardening on their camshaft lobes. Numerous cars suffered from lobes that would wear flat. If the exhaust lobe wears down, then the air-fuel mixture drawn into that cylinder gets ejected back into the intake and often ignites to cause the "popping" sound. You may end-up pulling the timing and valve covers to solve this problem. I'm highly skeptical that a camshaft lobe has worn out but there is always a first time for everything.
Take a good look at the ignition system before pulling covers. You may have a crack in the spark plug boots/coils that is causing spark to jump to the incorrect cylinder. An easy way to check for this is start the car, then use a trigger-spray bottle full of water to mist the spark plug wires and coils. If there are cracks, the car will suddenly run worse and you may hear a "snapping" noise. You may even see the spark jumping. You may have to do this when it is dusk or dark out to see the spark.
Dave Keller
1995 Contour SE
1999 Contour SVT
