1999 Plymouth Breeze Reflashing the Computer

I bought a car from my uncle, that night at heindls his business he had to switch out the computer. Then he let me drive it, and everything. That night I wouldnt go that fast at all, I would have to press the gas all the way down to actually start going FAST. Its like if you stop at a red light, then start going again, it would go slow for a few seconds, and get bad speed. It got up to only like 65. I know in cars you dont need to press the gas down that much to go like 45, but you had to press my car's gas down alot to get to 45. So I kept having to floor it. Is this problem because of not reflashing the computer? Thats what my uncle says, and now I need an new engine, because their was a knock in the rod. He says that theirs a knock in the rod because of having to floor it, and I had to floor it because of the computer not being reflashed. Is this true? Thank you.