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I've seen a 4.6 with a 5-speed with the 97-03 body style, but I'm not sure if it was available all of those years.
It sounds like they stopped selling them because there was a very small take rate on manual transmissions. My personal opinion is that the take rate was lower than it could have been due to packaging an automatic with other features buyers wanted. It became not worth the time and cost to design trucks with manual transmissions for such a small percentage of sales. Additionally, I'm sure emissions and fuel economy factored into the decision as well, not only in the numbers, but in the cost of calibrating and certifying a second system.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.