Sorry, that is a bit confusing. I don't think you can use the 3.0 bellhousing with the exhaust in the factory location, as it will interfere with the clutch slave cylinder location. The stock crossover pipe can be flipped to either side by simply cutting it and rewelding it how you want.
So with the stock exhaust you'd have to use a 3.4 bellhousing, and with a flipped exhaust you'd have to use a 3.0 bellhousing.
There is a lot more information to be found over in the 3.4 swap section of yotatech. Probably not many buggy builds, but there is good information about the engine itself.