sounds like you have a pretty good grasp on what is involved already....just thought I would throw in a couple of things I've noticed.
Mine is a 66, and I had to remove the egr spacer from the intake and replace the throttle body studs with new shorter ones...otherwise I was well into the shock tower area with the intake hose. This required fabricating a bracket to hold the throttle cable as the stock one bolted to the egr spacer.
We ran into the same problem with a 351W in a 67. If egr is important to you, you could probably avoid this problem by using either a SN95 style intake(or T-Bird) that has the bent neck upper, or using the adapter they make for the 87-93 style uppers.
Shock tower bracing is another issue, as the stock braces have to go. Again, Windsor-Fox steps up to the plate with a very sleek replacement, but I used an export brace and a spacer under it at the cowl and have good clearance.
I keep forgetting this, but I moved the battery to the trunk on mine(for weight distribution mostly) and it made it very convenient to route the mass air meter and filter into that spot.
Good luck. Doc.
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66 GT Fastback,fuel injected 5.0, 5-speed, cable clutch, JBA's and duals, 3.40 gears and handling mods...just call me "Doc"
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