Rattling Noise

Hi, I have a 1998 Honda Civic HX, 109000 miles, manual transmission. I just bought the car a month back. When I bought it at a Toyota dealership, they agreed to replace the timing belt and the CV boots before giving it to me. Ever since I got the car, I keep hearing rattling noises when I accelerate, it get louder when I go up a hill. Also the gas mileage of the car was not good, I was expecting somewhere between 30-36 mpg, but I am getting 29 mpg. Also the check engine light came on shortly, the code was P0420, "Catalytic Converter below threshold" So I took it to a mechanic, he said the timing belt is off by two teeth marks. He also said that the check engine light and the low gas mileage are caused by the wrong timing. Then, I took it back to the Toyota dealership, telling them the situation, after looking at the car, they said that the timing belt is installed correct. They also said that the timing belt on the civic can be installed only one way, if installed incorrectly, it wouldn't work. I thought that it could be pinging noises, so I put better gas, 93 octane gas, didn't help. Can you tell me what's going on? Do I need to fix the timing belt, or replace the Catalytic converter? Thank you.