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I'll bet it has to do with the differences between the Tunnel Port heads/intake and standard FE. If the bolts are spaced/located differently, your log would not be oriented correctly, and the mismatch would occur.
After rereading your post, it would seem that your issue is with the fore/aft location of the log?
If you could post pics, it may shed some additional light as well.
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CSX4068, '69 Bronco, '70 BOSS 302, '87 Mustang GT, '08 Roush Trak Pak
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