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We've always bought Hudson cases for this arrangement.

Hudsons are nice (some of our servers at Empeg are in Hudsons) but they aren't cheap.

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Not sure if there's a variant which takes non server boards.

A normal ATX board should work fine in an EATX case -- all the PCI slots, screwholes etc. are in the same place. It just won't fill it so much. This could in fact be an obvious way of fulfulling Roger's clearance criteria: if it's built for 12x13in boards and yours is 12x10in, that's 3in of extra clearance right there.

Peter