Everything in the long block is very similar to the 60s stuff. It has a one piece rear main seal and a roller cam. The fuel injection makes it much easier to tune for the street.
This is what we are doing with our Cobra.
Fresh shortblock with forged pistons
GT-40x heads x302 casting, unported, 6 angle competition valve job milled 40/1000s
Stock Cobra intake ported
Comp Cam 276HR.
The machine work is all done and the engine is shipping back this week for me to assemble.
We wanted it to look Cobra nostalgic, meaning no off brand logos or part numbers or Chrome under the hood. That was why we went with the GT-40x casting. I was always of the opinion that if you are going to go all out then tear up a GT, but the Cobras still command a little money so it's better not to go too crazy with them. We are hoping for around 360 fwhp. The limiting factor was the intake. It only flows about 210 cfm stock, so there was no reason to port the heads since they flow 249cfm unported. Ported the intake flows about 250cfm, so it should be a good match.
The best heads for performance are the Trick Flows, followed by the AFR lineup in my opinion. If it's an entry level head they are all about the same. The car comes with GT-40 iron heads, and they aren't terribly good. The preferred iron head is the GT-40p head that came in the Ford Explorer. It's more of a budget thing though. If you don't have a lot of cash to throw at it, you can get a low mileage Explorer engine out of the junkyard, slap a cam in it and go. If you are going to throw any money at the heads, ie portwork, or valve job, it's more cost effective to just go with aluminium ones.
It's all personal preference and budget though. Anything too radical and you have to start looking into a new transmission which gets pricey real quick.
Kurt