ordered PI Intake for 2000 GT, HELP

You are already PI

This is quite confusing.

But:

You have a pi intake (and motor) already. although it is an earlier all plastic version. The two drilled holes are for coolant sensors from earlier models. Your car has one. The other one will have to be plugged with something... like another aux. coolant temp sensor for a secondary gauge or something.
The extra parts you purchased will not need to be used, just say they are extras now The only things you will need are the new intake, and some coolant. (you can replace the intake gaskets, thermostat and o-ring, because you have new ones but it wasn't 100% needed)

I think thats all...

he needs the new intake and alternator bracket, thats it besides new gaskets.

that doesn't look like the OEM manifold