The thing is though, Before I put the car back together I checked to see if all the marks lined up. Everthing looked perfect. The car also started fine after I had charged the battery for a few minutes.

If my timing was out wouldnt it also mean the car would run like crap, slower takeoff, etc. It runs perfect once its going.

I dont know :/ I'm going to take it down to the garage and see if they can do a alternator / battery test on the car. Even maybe check if oil is leaking onto the sparkplugs.