Just replaced the alternator on my 2004 Lincoln Navagator everthing is working fine but the heat and air controls for the seats. Any suggestions? Checked the fuse and are ok.

Your best bet would be to take your vehicle to a qualified repair , before you start replacing parts you don't need too . Having a professional or factory ford IDS scan tool hooked up to check for DTC'S - diagnostic trouble code's would be the first step in the diagnostic procedure . Not guessing an replacing parts , you have no clue how to fix this , an your not going to learn how to here .
The climate control seat system is able to heat and cool the front seats. Each climate controlled seat is operated by push-buttons on the EATC module located on the instrument panel. Each front seat temperature is then monitored and controlled by the dual climate control seat module (DCSM) located on the passenger front seat track.
The climate controlled seat system contains the following components:

• EATC module
• DCSM
• Thermo-electric device (TED) and blower assembly within each front seat cushion and backrest
• Air filter (attached to each TED and blower assembly)
• Cushion and backrest manifolds
• Cushion and backrest foam pads
• Cushion and backrest trim covers

The heater element maybe burnt . At the control module connector pin's H & G . yellow with blue trace wire And blue with a orange trace wire , use a ohm meter an check continuity between these two wires .

Check the heater hose's going into the fire wall for being hot ! You don't need to know coolant circulation diagram . If the heater hose's are hot , problem is inside , temperature control actuator ! How to Fix Car with No Heat Easy

Try to change main control system

Have you checked the height sensor ?

there is a heat /cool control module under the drivers seat.

Always check body grounds. You may have good power to the engine with a good ground still, but your body grounds control power to all else.

check under seats to see if they are plugged up

Your best, with a Continental or Lincoln Navagator, to just
replace the air suspension with conventional shocks/struts,
after your vehicle is about 8 years old and you have put
time and money into previous air system problems

Strutmaster you hear a lot of and there has to be others

Check and make sure that the gear relay teeth are not broken