The two-headed variety looks to be a smarter version of the standard variety, with an extra bite attack. I strongly suggest that we drop the second boulder attack for these things, as that will boost their damage far outside their relative power level. Besides, just because it has an extra head doesn't necessitate doubling all potential attacks.
That's more or less my thinking. Just give a Common Roc the same intelligence, language and rock-dropping as a Great Roc and we're most of the way there, plus the two-header is also slower than a Common (24" like a Great Roc).
The only significant mechanical difference is the 2-headed has 16 Hit Dice.
Do we want to keep its HD lower than the similarly-sized Common Roc?
Most multiheaded 3E monsters I can think of have more HD than their monocephalic brethren, so we could consider boosting its HD to 20 or 21.
If we go for 16HD we'll have to decide which of a Common Roc's feats to drop.
I would drop Alertness and boost its racial bonuses on Spot and Listen, since it has two heads to watch for enemies.
I'd also swap its Wingover for the Hover feat, so it can fight like the 2-Headed Roc Harryhausen animated in the film
The 7th Voyage of Sinbad - striking out with talons and beaks while hanging in midair.
Not much else to do apart from change its flavour text.