I can't speak to the fit in a GT40, but I did just complete this install in a Cobra and it fits under the hood. You said throttle body so I'm guessing you are thinking EFI versus carb.
This Holley unit is tall (4 barrel style single plane intake with fuel injectors in the ports) but I did 2 things to make it fit. I milled about 3/8" from the top rear of the intake throttle body flange to reduce the rack/angle the throttle body and thus the air cleaner. This aligned the oval air cleaner to sit parallel with the hood scoop given the angle the engine sits at. Secondly, I made a new bottom plate for the air cleaner that is flat versus the 5/8" raised plate that came with it. I also had to trim some metal from the linkage where throttle cable attaches so it would clear the lower base. There are thinner oval air cleaners available but I wanted the thicker 2 1/2" thick filter element for the greater air flow.
If you really wanted/needed to lower the throttle body/air cleaner, there's about an inch of material in the intake that could easily be milled off in addition to what I removed. I don't know how this would affect performance (reduced intake plenum volume) but it would be only an air flow thing as the fuel is all introduced downstream of the single plane plenum. The 4 barrel throttle body is rated at 1,000 cfm so it flows plenty from that perspective.
I've only had this engine running for about a week now, but I have to say I'm impressed with it so far. The installation, startup and initial EFI tuning has been without any real challenge. I did purchase the unit from Prestige Motorsports and they loaded the Terminator X ECU with a base tune. It started right up, idles fine, A/F quickly adjusted itself to about 13 to 1 range and the engine runs/performs right up to expectations. I've only driven a couple hundred miles so far but it accelerates great and is very drivable without any quirks. The 347 cid engine dyno'd at 427 HP when built so it's a decent output for this size engine. I need to further break in the engine before pushing it into the high horsepower part of its range.
I hope this helps answer your question.
