TTT ANYONE HAVE ANY IDEALS?
You've already been given plenty of ideas and haven't reported back about most of them.
Double check your spark plug wiring... and let us know what you find.
Check your cam sensor and wiring... and let us know what you find.
Also, let us know what you find out when you try that other alternator you said you have.
Does it actually start? Does it run ok once started?
What about injectors... are you using the injectors from the old or new motor? If your using the new injectors, are you sure they are the same specifications?
What about the fuel rails... new ones or old ones? I hope you are using the old ones if your car was originaly a return system.
Are you sure you have the vacuum line connected to the fuel pressure regulator (return system) or pressure sensor (returnless system)?
Are you using new spark plugs?
I would go over the engine and take another really good look at your wiring and vacuum lines to make sure everything is connected properly.
Get out a hanes manual or something and double check your spark plug wiring.
EDIT: Also, are you using the new or old MAF sensor?