B heads are split/swirl ports, C heads are tumble ports. 03/04 heads have a better short turn radius and a few other things to make more power. 05 Aviator heads and all FRPP heads were 03/04 style with 8 thread spark plug holes. Intake manifolds are different between B and C heads as well and are not compatible. Then there are the IMRCs on the B headed cars as well as the issues with the secondary ports getting all crudded up because there is just air and no fuel going in there. An EGR delete can help this immensely though.
You will hear from everyone that "omg B heads flow more=better head". This is a load of crap. B heads technically do flow more at the very top of the RPM band but unless you are running a metric assload of boost this means nil and even if you are... it still means nil. With that said, B heads are way more plentiful than C heads right now and they can make great power, you just have to run a steep gear because they are a bit anemic down low.
edit: Also, you can get B heads for free if you look. Don't pay for them. They are a high supply, low demand item if those are B heads the guy is trying to sell.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.