I'm still contemplating multiport injection, and while it's somewhat of a pipe dream at the moment, I do intend to do it sometime in the next few years. With the possibility of a turbo in the future, and hopefully I'll having access to a welder next year, it has me thinking about the possibility of fabbing up a custom intake. Most throttle bodies seemed to be in a down-draft orientation on stock applications, but is there any reason that they have to be oriented this way? Seeing as how air is the only thing passing through them, it doesn't seem that they would know and/or care... I know a few people have gone the custom intake route; are there any good resources regarding manifold design?

No reason you have to use a downdraft throttle body! See Here. Also, Ray (Rayman440 on here) who runs Mopar Market Forum in Australia has done an absolutely sweet triple-sidedraft EFI setup.

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