Rough idle after initial startup.

1995 Lincoln Towncar Idle rough now check engine light on?

Really the sky is the limit here. See when you first start vehicle the computer is in open loop which means it is not monitoring the O2 sensors and fuel control is set to a calibrated setting. After the Heaters heat up the O2 sensors it then goes into closed loop and starts monitoring the O2 sensors to control air/fuel. So anything in the fuel and air mix could be causing your problem like false air volume reporting from the MAF sensor,a vacuum leak,unmeasured air getting into the engine behind the MAF sensor from a leaking hose,,a faulty pcv system,lazy O2 sensors, etc.
I would first recommend cleaning the MAF sensor and resetting the keep alive memory.Get a T20 torx bit and remove the MAF and get some electrical cleaner and spray the MAF bulbs clean then let it air dry or blow it dry with light shop air. Then disconnect battery for about 30 minutes to reset the strategies and see if this cures your problem. It will take probably 50 miles of driving for the strategies to reset.