Okay, here goes...
I've had a 418 ci Windsor under a 98 Cobra hood and it cleared. However, it was a HUGE PAIN IN THE ASS to get it that way. Here's how to do it:
1. Install drop solid motor mounts made by HP Motorsport
2. Minimize the distance between the mating surfaces of the upper and lower intake manifolds. In other words, forget about having spacers. If you have spacers or nitrous plates like I did, this will become a bigger PIA.
3. Ensure the air inlet for the TB drops down below the horizontal plane of the top of the TB as soon as it exits. The difficulty is not in getting the motor to fit, but getting the air pipe that is attached to it to fit. It will hit part of the triangular support brace on middle of the an OEM Cobra hood. I had a custom pipe made, which is in the attic now I think. I used a SN95 TB adapter and a 75mm BBK TB.
You can also use a low-rise intake like a Cobra or something and a C&L air inlet tube. Like I said, it just needs to drop down as soon as possible.
Here's a picture of the first 351 in the car, followed by the 418.
Once I switched to a 4" air inlet pipe, it was all over. No amount of milling, cutting, and other headaches would make it work. That was a sad day because I really liked my Cobra hood.
Paul.