okay so the mechanic told us it needs a new motor, the dealership agreed to paying for the new motor which i couldnt believe! Where can you find motors online? We are worried about them trying to put a fake cobra engine in it. Or putting one with high miles in it. The dealership also had no idea that the check engine light had been unplugged they weren't happy about that at all. I guess the new engine will solve all of the problems, but i am not sure. Is it even possible to order a brand new 2001 cobra engine from Ford?
1st - What was wrong with the motor ? Was there something mechanically broken or how did they come to that conclusion ? You want to make sure they are not just "throwing parts" at the problem and find out the "why" or the diagnosis.
If it needs a new motor (depending on what "broke"), an alternative would be having the same factory one, properly re-built by a local shop who is familiar with building 4v cobra engines (if this is even an option). That way, you get to retain some of the "original" engine with the car, if you are truly worried about "numbers matching" and all that stuff (which is sorta a moot point nowadays, but that's besides the point).
2nd - Ford will most likely replace the factory engine with a freshly assembled remanufactured engine (ask about the engine warranty). IIRC, it's been a couple of years since Ford had any leftover '01 or '00 4v Cobra engines available (not talking about the 2000 Cobra "R" engines btw, talking about regular 4v engines simply manufactured in the year 2000 or 2001 - that throws some people off).
It's hard to locate any "new" old 2001 cobra engines online nowadays, unless you find a private party/someone who purchased one a few years back and crated it in their barn or garage. A place here in MI called KarKraft was a pretty big retailer of "new" old engines (and other OEM Ford stuff). Not sure if they are still around (?) though. I remember they had a huge garage sale a little while back - maybe closed their doors? Google them.
Chances are better for locating a used (with mileage) Cobra engine from a wrecked car - which can be hit or miss, would be wise to inspect it prior to purchase/installing it.
If they are offering a limited warranty on the reman engine (via Ford), which they should, and the Ford dealership is handling the swap/installation, maybe it will turn out OK. Or maybe it won't.
The problem is that you guys really won't know if replacing the engine will solve everything either (in case it winds up not being the source of the problem). Auction cars can definitely be risky because the previous owner can't be contacted for information on what was done to the car.
If it's still not too late to walk away from the purchase, you might want to consider doing so, as this car will probably have other gremlins waiting to sneak up on you down the road. I surely hope not though, but be prepared.
FWIW - As far as the engine builder plaque found on the passenger side engine valve cover, you can re-use the valve covers from the factory engine on the reman engine (or ask about swapping the build tag over perhaps, to try and keep it looking like the factory engine on the exterior of the engine, if that really bothers you guys).
G'luck.