Intermittent climate control problem

I have a 99 century that seems to not like to blow warm air into the car when its cold out. Can't figure out any rhyme or reason for it but it seems like all the vents are in a closed position and the fan is just blowing air around inside the dash. It generally only does it at highway speeds. The vac lines have been checked and appear to have no leaks. Also does anyone have a got VATS bypass solution? My wife is tired of being stranded and having to jostle the steering wheel up and down to get the car to start. All i see on other sites is arguments about viable solutions to the problem and no real clear way to eliminate this headache besides buying a Ford.

since temp is electrical, and modes are vacuum, you may have a bad HVAC control head.

By "checked the vacuum lines", are you referring to the ones under the dash, or under the hood? There is a vacuum line that runs from the engine near the alternator, down the fenderwell near the battery, then through the firewall. This is a hard plastic line that very commonly get's broken if any hamfisted work is done around the battery, and can also deteriorate with age and crack from vibration. There is also a vacuum storage canister under the dash that holds vacuum pressure for low vacuum times like hard acceleration. If this canister fails, it won't hold position (vent, floor, defrost, etc...) and will default to 1/2 floor 1/2 defrost. Temperature is controlled by an electric motor mounted to the drivers side of the center console high up under the dash..

The Vac system was checked by my local shop and they said it was okay. It seems like because it generally only happens at highway speeds there might be a problem with that canister. How can i test it myself to see if it is leaking?

a hand vacuum pump to apply vacuum on one side, and a vacuum gauge on the output side will show if it's leaking. At steady cruising speed, the car has sufficient vacuum, but if the canister leaks, it may slowly bleed off if the leak is bigger than the engine can overcome. This still would not affect the temperature of the air, only where it is distributed.

As for the PassKey II system, the problem is frequently in the wire harness in the steering column, particularly where the ignition lock cylinder rotates and flexes the wires constantly. You can remove the column trim covers and inspect the wire harness for apparent damage, then repair any damaged or frayed wires you discover. A new replacement lock cylinder includes the magnet, sensor, key, output module (switching transistors), and the wire harness all the way to the bottom of the steering column.