Maybe the head was rebuilt, but was it checked for cracks??? This is not done automatically, but should be.
Jim's referring to cam timing, was it set correctly? Very critical. I'd pull the valve cover off and check it again, if the engine is not assembled correctly, it can come out of adjustment at startup. Was the head torqued correctly? What torque method did you use? I've also seen plugged pre-cats cause complaints like this (except the alternator problem), you may want to try running it with the front pipes loosened from the exhaust manifold and see if it runs better.