I checked mine for you. It's right around an inch clearance at the leading edge, which is the tightest, with the production 5.0 intake cover installed. Way more without the cover. I'd be surprised if the Boss intake didn't fit.
I wasn't sure from your post if you have a take-off engine from a Boss or just the intake for your Coyote, but if you are just contemplating putting the intake on it will only hurt you up to about 6500 RPM. Even with the right tune up it will be a negative up to about 5500 vs. the production intake.
90 Mustang Coupe (9.44@143, all motor)
2011 5.0 Convertible Roush Stage 2 (635 HP)
03 F-250 PSD
06 SRT8 Magnum
FFR 33 Hot Rod #487
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