Help a newbie out, 2zz swap.

Hi, I'm going to be doing a 2zz swap(hopefully) and need to get some things sorted out first. I've searched and found out a lot, but there's still some conflicting things I need to clear up.
I know the 5speed will bolt up to the 2zz, but does the ECU care? Will the fact that its not a 6speed cause problems?
I've heard some people say the exhaust manifold doesn't bolt up directly with the mid pipe, how far off is it? Could I bolt up the header from the 1zz to the 2zz and skip this problem?
Everything else as far as I know is a direct bolt up, I'll need to buy a 2zz flywheel because the engine doesn't include one, but is there anything else that will give me problems in this swap?

Im not the car owner, my cousin bought a 2000gt 3 days ago, and it blew the day he got it... so I told him I'd help him out with the swap to save him money. Funny thing is, he bought a golf 2 weeks before this, and its driver side wheel broke off(the seller actually took it back though!).

I want to start this out on sunday or monday, so I'll be checking back here lots. Any help is appreciated!