So I need to replace the engine in my civic ,
As far as engines go it shouldnt matter if its from a at civic or a mt civic ?
Like it shouldnt matter just us my intake manifold from my orginal engine wiring harness and so forth?

 

To my knowledge it shouldn't matter as long as your only replacing the block, But if you want to switch from AT to Manual you will have to make some other modifications to make.

What motor is in the car ?

 

Its a d16y8 in the car replacing it with the same,
the engines from a auto, my civs a manual I just gotta take the flex plate off and attach my clutch assembly and what not to that ?

 

And change the intake manifolds as you said.