Thanks guys!
Talked to the garage again today, apparently the injection pump (the expensive one is bad too). So it looks like I have about a $1000 shop bill, plus the computer, and plus the aftermarket pump. I bought an aftermarket pump, told the one owner that I didn't want a stock pump put on. The other owner went ahead and told the shop to put on a stock pump anyways. That same owner tried to tell me he wouldn't pay for my aftermarket "shit" after his brother, the other co-owner, told me they would. He was misinformed and made himself look like an ass on the phone. I talked face-to-face with the both of them the owner back tracked all over himself and took back everything he said on the phone in a round-about kind of way.
He then went on to tell me that I shouldn't have been as involved in the ordeal. I guess I shouldn't have talked to my car salesman, who then told me to go to one of the owners, who then told me to talk to the garage about a part. Finally I talked to the actual owner, or finally told me that I shouldn't have talked to all these people and that I made it too complicated. (Which is funny because I did exactly what the representatives of his company told me to do.) A few choice cuss words were exchanged between parties and now I guess I owe $1000 to the shop, and they may or may not my extend my warranty.
(Sorry this is so long, and probably not well written, but I am in a shitty mood and had to kind of rant for a minute).