hesatation/chech engine light

I recently freshened up my motor. Upon re-installing I also added a MSD 6al box,MSD distriutor and deleted the a/c. I had a check engine light before I even freshend up the motor but it is still on. When I push the gas it hesitates then puts you into the seat. I also get a slight pop every now and then when I rev the motor. I had the car hooked up to a snap-on computer that a mechanic friend had and it came up with about 13 different codes for EGR and one for the Mass air flow sensor. I thought about deleting the EGR. Wont this trow a check engine light too? I know that the check engine light could be the EGR but what is the hesitation coming from. I had the heads shaved
.017 and also had the rings re-cut for the lockwire head gaskests. I made sure to do everything to the T when it came to torque and patterns when putting it together. What am I doing wrong? Any ideas, because I'm out.