Well I called up the machine shop today and talked to the guy. I must have been in a daze when I picked up the engine and I thought he told me he made his own marks on the gears. He told me the stock notches should macth up in order for the timing to be correct. I must have misuderstood him. He said he didnt port anything out enough to make it idle lumpy. So now I know for sure the timing is out of wack on my car. I am relieved to find out that its juts a small problem that can be fixed easily.
Update on the CEL's...
Today I gave my car a bath. It was so dirty after sitting out side for 2 months. So when I was cleaning up the engine bay I decided to reset the ecu by unplugging the battery for about 20 minutes. Well I have gone 5 miles since then and I have no CEL at all!!! Maybe my car was just acting up because of the new engine parts or something? It still has the bad idle but I dont care. Its going to be fixed soon. My car looks sooo much better since I washed it.