1999 Honda Accord several issues

Well. Im a whole 19 yrs old. Ive owned this honda for a year and ive had a few problems with it. Generally speaking ive been told that hondas the best car on the market lately. Well, it started with a flat tire. Then moved to a knocking which I attempted to take care of by returning it to my dealership. They said that it was a normal honda knock and I just dealt with it because I knew they were going to fight me over this knock. Then I got a clunking noise in my passenger side and had it taken to my dealer again and they claimed it to be an outer tie rod end and sway bar. Well it was assumed fixed when I drove off the lot. A few months later it came back and now the warranty on the parts is gone. Then it went to a check engine light that turned out to be an emission part and I had to pay for it to be replaced. Yet the light is back on. Now when driving my car it starts hard and its noticably louder. I looked for possible holes in the exaust and havent noticed anything but when I rev the engine to 2k rpm it picks up on time and delays for a second. Then the muffler changes tone and slowly goes back to its usual idle or even lower. The usual idle speed for my car runs between 1k and.75k rpm depending on whats running in the car. Im not sure if all of this is related but I need to do something soon. Its beginning to worry me that the car will leave me stranded on my way to work or even back from work which would be even worse. Especially getting out a 3:00 am. Any possible advice would help alot and give me a direction on where to start. Thank you for any help you can be. I really hope that its nothing too serious because im not under my extended warranty anymore