Clint, I was using a set of Hooker Super Comps and the issues I had were:
1. the #1 primary hitting the pitman arm retaining nut
2. clearance for the upper control arm mount bolt
3. the collector on the right side touching the floorpan (because it was indexed differently than the left side)
4. couldn't run a 3" air cleaner (but I was also running a tall single plane)
All the fixes were pretty easy, it was a matter of 'massaging' the headers and running a K&N X-stream lid. Another thing to keep in mind about the Iron Eagle tall deck is that since the pan rails are spread .800", there's no provision for oil filter built into the block, you have to run a remote oil filter. No biggie, though.
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