1998 Ford Expedition Emergency break is not working and break does not work right

If you hear the relay, you need to pull the door panel and check power at the motor. Power there replace it. No power, the wires tend to break in the rubber boot at the front of the door jam.

Cause could be from a worn out multi-function switch (blinker switch)
Filaments heat and expand and decrease in size as current runs to them, basically making and breaking a circuit several times, creating an intermittent switch that supplies current to the lights. These can go out, and will need to be replaced.

check fuses. if all good there i would use a test light to check power to brake light switch on pedal. should be two wires. one will be hot all the time and the other will be hot when brakes are applied. if you have power there and no lights still i would suspect multifunction switch is bad on steering column.

bad ground or relay. emergency lights run on a separate system

What does "not running right mean"? at the most, put in the fuel injectors from the old engine. You may have gotten Flex Fuel injectors? I would tell you to have the dealer or a garage that does a lot of Ford work check it out.

Most have an emergency button to open it...crawl in the back and look at the center of gate for a removeable insert at the center of gate ....some look small and round...others may not..It should just be a small button...just push button and gate should open...owners manual should show this...
some may not.

It should be located on the blower motor housing under the right side of the dash, it will have wiring connector and 2 screws holding it in.

You need to replace your brake light switch which is located on your brake pedal. The reason that the right and left are out and the middle isn't is because there are two sides to the switch for vehicles with three brakes lights. It is a very easy part to replace and is relatively inexpensive. Change that switch out and you will be good to go. Let me know if you have any other questions. Thanks for rating my response and for using FixYa!

i changed this on mine its pretty simple. disconnect battery,remove plastic caps off back of steering wheel i think its 8mm bolts holding on your air bag remove and disconnect , pull your steering wheel and its right their you'll have to take off the plastic cover that goes around your ignition switch. the wires run down the column there is 2 plastic retaining clips that u can pop open with a flat screwdiver underneath by your brake pedal there is 2 plugs a brown one and black one . be careful when installing make sure u have it lined up and don't pull the yellow plastic ring out till all intact or when u turn it'll break again. it took me about 1hr 15min to replace

Do you mean the shoes inside the brake rotors?