i see that many of the engine harness plugs from the crx si needs to be extended to fit the Intake manifold . my question is can i use the Intake manifold from the D16a6 instead of the z6. And how does it affect me when it comes to emissions. Thanks!

 

I'm pretty sure the Ref will catch that difference and reject ya. They're really strict about the vaccum diagram. I don't have one in front of me, but i do believe they're slightly different.
If you would like your harness rebuilt for that engine, and to pass ref, checkout the Optional Modification Package on Rywire.com.