no prob,
in the above photo the only part of the engine/box that is lower than the bottom chassis rails is 25mm of the gearbox bell housing, the sump of the engine is flush with the lower chassis rails, but i have used a shortened sump from a zetec engine, so it all depends on how much your sump is shortened by, to how much clearance you have below the engine.
when fitting the engine/box..... try to keep the output shaft of the gearbox level with the center of the diff flange
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cheers
andy