Hey guys can a the head from a Manual transmission engine into an automatic engine block a or a broken stud in the distributor affect the ignition timing?

I just did a head gasket job in my 97 Civic LX D16y7, in the process I installed a new timing belt kit and used a spare head from a my manual 99 Civic DX.

At the moment the issue that I am having is that the ignition timing is off, and I am not able to get in spec using the timing light gun. in order to get it closer to spec 12* at Idle, I have to rotate the distributor towards the back to advance the timing and even then i can only get it to lined up with the TDC white mark.

I know that the mechanical timing was done right because I double checked the crank and the cam timing marks after installing the belt. and double check it by verifying the bottom TDC white mark indicator in the harmony balancer and the cam timing marks were all lined correctly before I tightened the tensioner bolt

So I am suspecting its either

1 The broken stud in the distributor(Something that the PO or his mechanic did)

or

2 The head manual engine head is some how different than the automatic even if they came out of a D16Y7 block.

What do you guys think? At this point I am thinking to remove the timing belt and realign verything again.

 

Your mechanical timing is likely off by one tooth.

Remove the valve cover and upper timing belt cover.
Rotate the crank pulley 6 revolutions counterclockwise until the TDC1 white mark perfectly aligns with the pointer.
Use the rear-side cam pulley marks to check whether they now align perfectly with the top surface of the head.

 

Yea I am having that on my accord as well