The problem with the rear end being higher than the trans output shaft is that the working angles increase when the suspension compresses. So if you start out with a working angle of 3.5, under full compression it may go to 5.5.
This is exactly why you see people on here cutting their tunnel to get the tailshaft of the trans up higher. That will allow for more conventional and smaller working angles. The more severe the working angle, the more they tend to vibrate as speed increases.
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Todd
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