Rough idle and rough when driving

engine light flashes ???? Your best bet , take it to a qaulified repair shop , right now , damage the catalytic converter is happening .
Flashing check engine light CarMD

Fuel pump

check for loose/ missing vacuum lines on the engine . Easy enough when replacing an engine.

check coil packs

you have a possible vacuum leak somewhere or maybe clogged egr

Here are the most common causes of idle surge, rough idle esp when cold, other symptoms include stalls at stops, slow idle speed, erratic idle speed, rough idle and engine hesitation (and other problems), it is in most cases the idle speed control air-bypass valve and or throttle valve and upper intake, these area's get full of gunk and combustion residue over the miles and cause idle issues (stalls, low idle) like yours, Get a can of intake cleaner from any local parts store, not carb spray, intake cleaner, it is made by a company called CRC, remove the air intake hose to the engine, hold the idle high so the engine won't stall, then spray the can of cleaner into the intake while keeping the engine running, use at least 1/2 the can, shut down the engine and disconnect the battery for 5 minutes, then restart and complete a number of mixed driving cycles, town, freeway, stop and go etc., after a few days the problem will go away as the system will relearn to the clean intake

1997 escort idles rough, the first thing is to make sure the throtlebody plate is clean. This sounds like the idle may be staying to low at times if it smooths out with ac on, when the ac is turnned on the computer raises the idle a touch to make up for the strain on the engine from the ac compressor, clean throtlebody and look at and clean idle air control valve, if this valve is not controlling the idle when needed the engine will idle lower than normal and cause a rough idle.
Another thing is the sparkplug wires, take a look at those, if at night or with a good eye use a spray bottle and spray a mist over the wires and watch for any sparking, this spark may be very small so look at each wire closely or may be big enough to see and hear. this is where i would start. good day.

This whole problem is most likey due to a sludged up intake and idle speed control valve, do the following procedure and it should take care of the problems, also run a couple of cans of LUCUS brand fuel injector cleaner through, I know u will see it is more expensive than other brands, but the thing is it works!
Here is the most common cause of surges and stalls at stops and low erratic idle speed and rough idle, it is the idle speed control air-bypass valve and throttle valve (IAC for short), they get full of gunk over the miles and cause idle issues (stalls, low idle) like yours, Get a can of intake cleaner from any local parts store, not carb spray, intake cleaner, it is made by a company called CRC, remove the air intake hose to the engine, hold the idle high so the engine won't stall, then spray the can of cleaner into the intake while keeping the engine running, use at least 1/2 the can, shut down the engine and disconnect the battery for 5 minutes, then restart and complete a number of mixed driving cycles, town, freeway, stop and go etc., after a few days the problem will go away as the system will relearn to the clean intake

there are 2 things that usually cause this, one is a dirty intake idle control valve and the other is hard engine mounts, I would say that both most likely apply to your car. try cleaning the intake with the following procedure from Ford.
Here is the most common cause of surges and stalls and low idle rough idle, it is the idle speed control air-bypass valve and throttle valve (IAC for short), they get full of gunk over the miles and cause idle issues (stalls, low idle) like yours, Get a can of intake cleaner from any local parts store, not carb spray, intake cleaner, it is made by a company called CRC, remove the air intake hose to the engine, hold the idle high so the engine won't stall, then spray the can of cleaner into the intake while keeping the engine running, use at least 1/2 the can, shut down the engine and disconnect the battery for 5 minutes, then restart and complete a number of mixed driving cycles, town, freeway, stop and go etc., after a few days the problem will go away as the system will relearn to the clean intake.

check the egr valve it sound to me that its stuck open and if this happens excessive exaust gases are flooding the intake or you might have a vacuum leak either one of these problems will make a high pitch sound