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What I meant by being in the same plane is that you should be able to draw a straight line between the two yokes. A downward slope from the tail of the transmission to the differential is fine and is quite typical. What you do not want is the tail of the transmission sloping upwards and the differential at neutral or sloping downwards. You want to avoid any compound angles in the universal joint. Use a level. If both ends are level, but one is lower than the other, that is fine.
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