Im about 1/3rd way through the Dawngaurd quests at the part where you sneak into the Castle and find Serena's mom. But I finished the vampire quest line on my other guy and so far there is no difference at all besides the beginning and the side quests. Besides Crossbows, armored trolls, armored huskys, side quests, death hounds and HQs are there any differences?

its alot like the Civil War quests. They are almost the same with minor diffrences.
while your filling the blood chalice with VL your recruiting followers for DG, Both quest lines have you do the moth ritual, and the initiates ewer quest. same ending as well ( i wont spoil ) but with all the radiant quests they are varied.

Hope this helped