2008 Mitsubishi Eclipse Questions

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The check engine light came on for the first time since she had it could that be from a bad throwout baring putting a strain on the engine??
How much is a wire harness for a 2008 Mitchubishi Eclipse Spyder with a 2.4 in it And can I take the motor from it and drop in my 2004 Lancer ES
The inside of my Spyder burnt completely up! Only motor and the body is left that is good. But everything on inside is completely burnt. Where is the computer located on this vehicle
My wife was in an accident in her eclipse. Didn't do much damage but it set the air bags off. Now the fuel pump doesn't come on. Is there a reset for the fuel pump? Or is it in the computer?
Sometimes when I drive my check engine light will come on and the transmission won't automatically shift out of gear. I have the paddle shifter and today I put it in the manual setting and I couldn't get the car out of third... Put it back in the automatic setting as well with no joy. There have been times that I can shut off the car and it will go away. I have noticed at times this problem happens if I go over rough railroad tracks or hit a pothole. However it happened today after I had the oil changed... Because its intermittent I was thinking maybe something electrical under the car is going on? I need help and answers... I don't want to shoot from the hip and drop thousands of dollars blindly. Any ideas?
I gained access to the interior of the car since then but the alarm is now active and I can't get into the trunk to disarm alarm system.
The window is pulled away from the top, how can I repair this? Is there a specific type of glue, to use. The strip it was attached to, only an inch on top & bottom of window, which is just a flimsy piece of vinyl, approximately 2 inches wide. Any suggestions, at least to get it through till spring.
Took car to dealership an had timing belt,balance belt,water pump, an fuel replaced. The transmission worked fine when car was taken in, now park, an reverse work but when put in drive it doesn't pull and the drive indicator light doesn't light up. However, you can pull the A/T fuse and it will drive but I only have 3rd gear and service engine light came on. Any suggestion?
when you a person have there timing belt changed on one of these cars?
Was told after getting an inspection of my brakes and having symptoms of high-pitch squealing and pedal going very low to floor, but they still work (just not as well as before)that the master cylinder and possibly the booster was defective and needed replacing. However, on this site I read that a code light should come on for bad master cylinder. Also, how much should it cost for a complete repair of a master cylinder and booster?
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