You all are probably right when you all say that I should part the car out. I have decided to keep the car and have the mechanic rebuild the car. I am still in the positive side when it comes to the amount spent on the car. I had bought the car for less than $3500. With all the stuff that the car has I would end up really making a mistake by getting rid of it. The car has a wideband, double din cd player, sub, coil overs, upgraded radiator and some really good upgraded parts on the engine that can be salvaged. Oh also the Trans has that LSD upgrade. I will stick to the car and make it a reliable car, I know that I will still have to fix things here and there but I am willing to deal with it. I really have a great mechanic that know his stuff, this dude is so great that he has people from out of state bring him there cars. I will keep people posted.
You are not on the positive side and never will be. You bought the car for $3500, so that is how much it is worth. If you get it running properly and everything is in tip top shape cosmetically and mechanically, you might be able to get six or seven for it. There is no way you are getting that car running well for that ~$3k difference so you will inevitably end up with a net loss on the car.
Now if you part it out, there is definitely $3500 to be found in that car, plus you can sell the remainder for a bit too and come out ahead. You could probably end up a couple grand on the plus side, but it will take some work. If you are really industrious, you could return the car to stock with a used FS motor and sell it as a running good condition stock car for $5k, but you'll be playing a numbers game and finding parts and swapping them out will be a full time job.
If you continue down the road you are on, with someone else doing this work for you, you will spend many thousands, and you may end up with a very fast MSP, but it will be worth no more than six or seven grand. Mods that can be removed and resold are one thing, but labor cannot be resold. Every dollar spent is gone forever. Just ask the guy who sold you the car.
I would love for more people to come over and keep the Protege platform alive, more people like Maxx_Mazda and Brian_MP5T who have the expendable income and personal fortitude to make the car something truly incredible. But if you actually add up what they've spent plus the blood, sweat, tears, and ingenuity, there would be very few people out there willing to make those sacrifices for their Protege.
You have to treat it like an expensive hobby, and you are not just paying for parts, but for the personal satisfaction of creating something special. It should also not be your only car, because things are going to take longer than expected to get done correctly and other things are just going to break.
If that sounds like something you can handle, then the more the merrier.