The Gen 3 engine has a slightly larger cylinder bore than Gen 1/2. This accounts for the extra displacement.
I’d do more research but from what I remember when guys doing 3-2-1 builds, you match the head gaskets to the heads for their oil port. The actual cylinder sealing surface ring is always larger Than the cylinder bore itself
From what I see from other online sources, Matt James is correct. The gasket must match the head. The people who have done the gen 3 block with the gen 1 or gen2 heads have not mentioned any issues when using the correct head gasket for the heads. I hope this 100% true because I just ordered a short block from my local ford dealer this morning. They price matched the price from Tasca, which was the most reasonably priced dealer I found and I don’t have to worry about shipping charges. For whatever reason, Tasca wanted $1100+ to ship to my location. I have had full engines shipped cheaper than that so I’m not sure why it was so high.
The only heads that are compatible with Gen 3 blocks are Gen 3 heads plus '11-'12 Gen 1 heads (including '12-'13 Boss 302) that use long 12mm head bolts. The '13-'17 MY heads use shorter 11mm head bolts and are only compatible with '13-'17 MY blocks. If you're using a Gen 1 Mustang PCM for a Coyote swap into an '05-'09 Mustang (V6 or GT), your swap engine will need to have the Gen 1 camshaft drive system (timing set). This means you'd probably also need Gen 1 camshafts and Gen 1 heads. If you want to bolt these items onto a later generation short block, the '11-'12 items will only go onto a Gen 3 and the '13-'14 items will only go onto a Gen 2.
Thank you Dino. I bought a first gen coyote engine for parts and I will be using the 11-14 pcm. I have the first gen cams and stuff and I am going to put new gen 1 timing components on it when I assemble them. I believe I have an 11-12 engine due to the block having the piston oil squirters but I have been unable to nail down exactly the year. I have tried looking up the head castings and I have been unsuccessful. I will measure the bolts but is there a place that spells out the head casting and where I can find it? I’m 99% sure it’s an 11-12, but I’d like to be certain. The short block I will be using is a new gen 3 from Ford. The block from the gen 1 was scarred and needed rebuilt and I found it cheaper to buy a new one. Any help is appreciated.