are you running the stock or aftermarket suspension?
i have a 46o witha MII suspension and use Headman headers meant for a 77-79 4x4. the only modification i had to do was bend them out a bit to clear the steering shaft and use 2 u-joints to go around the headers. the passenger side fit perfect and both sides exits above the bottom of the frame rails so the collectors are tucked up nicely and don't drag.
if i was doing it again, i would probably spring for some block hugger headers like Sanderson makes. i think they would work a lot better with less modifications required.
I also run the Hedman long tubes on my 429 and clearance was not an issue but be aware that with the tie rod behind the axle, clearance issues can be a problem as in the tie rod hitting the tubes when the suspension bottoms out. Mark