"....transmission has 5 degrees of down angle and is much lower to the ground than the rear."

This right here tells you that all will be well because the trans output shaft and pinion can't be pointing toward each other if the trans shaft is lower. The driveshaft will be running upward as it goes to the rear and that's ok too, just as long as, like you said, you have the trans output shaft and the pinion parallel with each other.