Now that I'm thinking of it, I believe there is a simple but important procedure for proper cam timing when doing an M104 and it's a common mistake for first timers. Lining up all the marks is not enough, there an extra step involved. I think if you don't proceed correctly, the car will run okay when you're done but may set off timing trouble codes. You should really find out about it from someone who's done a few before you continue.