The pinion and tail shaft do not need to be parallel, they do need the same u-joint working angle. If the tail shaft is pointing down, and driveshaft is level, pinion can be up or down, as long as the working angle is the same. Next time you are around a long wheel base box truck, notice the driveline and how each driveshaft section is at a different angle.
Most race cars start with pinion angle lower and a steeper working angle, so under a hard launch ( load ) when the pinion tries to climb up the ring gear, the u-joint angle is still with in its range of operation.
Carburetors also do not need to be level as most engines are pointing nose down once all the weight is on the chassis. Get close and you will be fine, its not the end of the world if its angled.
Joe