When you're trying to drill and easy-out a busted bolt, it's always best to use a center punch to get your bit centered on the broken piece so the bit doesn't skip.
As for filling the mistakes....is that aluminum, or cast? And how big are the holes? If they're pretty big, I suppose you could use JB Weld, but I don't know if it'll leak or not. I'd think it wouldn't, but you never know. If it were me, I think I'd either pull the intake and replace it, or braze (or heli-arc) it back up, then re-drill and re-tap it.
If they're small (under 1/8th") and will be covered by the gasket and housing, you could probably just fill them with silicone and not worry about it at all.
Out of curiosity, why did you keep going when your bit skidded off the bolt?