It sounds like the company has been very fair to you. Most others car dealers would tell you good luck as you drove off the lot with the car. All vehicles are sold As-Is, unless disclosed with a warranty. I don't understand what your complaining about, but they've been more than fair with you in regards to this vehicle that you had purchased from them. It shows that they stand behind the vehicles that they sell, and spending $50 for them to replace the engine is nothing. All repair shops charge a diagnoistics fee and most charge between $65-$100. I would say that you made out very good here, and I would continue to make your payments so you could eventually go and get a nicer vehicle. If you fail to make your payments to them, and they eventually repo your car, you'll be stuck with a repo on your credit report and it'll hurt you for the next 7-10 years on obtaining credit especially in these credit markets today.
Good Luck!