1996 Mercury Sable 1996 Merc. Sable Mystery Check Engine Li

Engine Mechanical problem
1996 Mercury Sable 6 cyl Automatic 100, 00 miles

Hello,
A few months back my check engine light came started blinking. It only starts blinking under certain circumstances, though. When I have been driving on the highway, and then I stop, either at an exit or a toll and my RPMs drop, and then I start driving again, it starts to blink. It blinks for 5 minutes or so and then stays on, solid. When it blinks the engine idles a lot rougher, more vibration than usual, and the transmission doesn't seem to have the punch it should, though not incredibly underpowered. When the light is solid the car runs as normal.

The computer shows codes of misfires on cylinders 1 and 3. We gave the car a tune up, and then a new coil, to no avail. I brought it to a Ford dealership, and during their initial diagnostic they could not ascertain the problem, and they wanted additional money to do a further diagnosis, still with no guarantee of a solution, so I declined. They did say they suspected it might be a problem in the intake.

I was briefly chatting with a mechanic the other day and he mentioned that if it is something wrong with the intake manifold it would probably be around $1500 to replace and not worth it, but he suggested that sometimes on the taurus/sable there is a sensor which fails. I don't remember the name of the sensor, but it has to do with the transmission and the idle rates. He said that even though it is technically a problem with the transmission it causes the Check Engine light to come on and might spit out the generic code of cylinder misfires.

So my questions are: 1. What is the sensor he was talking about? 2. Is it in fact possible that sensor malfunction is the problem? Does anyone have any other ideas as to what might be causing it?