With all that work being done there's certainly plenty of opportunity to maybe not get something put back together properly. I would certainly doublecheck the timing belt alignment. Maybe it's off a tooth on one of the camms? What do you mean by "new air intake". Is this just a stock part replacement or a K&N type new system? K&N filters require an oil application on the filter which some folks say can coat the MAS sensor and cause mixture problems. How's the fuel pressure at the rail? Should be around 42 psi. New fuel filter?? Make sure all the vacuum lines are connected and also connected to the right fittings.