crankshaft sprocket alignment
 

I am hoping someone can help me. I am working on a mustang for a customer. It has a 4.6L and has been built up a little. It has only been driven a few miles on the new engine and the oil pump broke. while putting on the timing chains we noticed the crankshaft sprocket has several slots in it and was on 2 degrees R. I wouldn't think it shouldbe retarded. Is this right to get performance or should it have been at 2 A or just at zero? It dies at idle, wondering if it has something to do with the 2 R. Does the computer need reflashed if it isn't at zero or TDC?
Thanks

The cams should really be degreed in to be sure, do you know if these are factory cams or aftermarket. If they are aftermarket and have big lift and duration, you may have piston to valve clearance problems. (very common on modular motors)