Be careful, the candy is actually a copy of VPDS.
Anyway, hiya. Responses:
% is a shorthand for modulo, which basically means "divide and then look at the remainder". So, "var % 4" means "divide var by 4 and then look at the remainder". e.g. 7 % 4 = 3, while 12 % 4 = 0.
In the specific case of byte 04... let's say that a certain move (such as Punch) has a value of 129 (which would appear in hex as 81). 129 % 4 = 1, so and 1 indicates a normal priority move. The rest of byte 04 is a bit toggle, and since bit 80 (128 in decimal) is set, this means that Punch is subject to KO Throw.
Yes, for moves with linked abilities, their combo send data is never actually used. Instead, the combo send data of the linked ability is used. This essentially means that the combo send data of certain moves is never checked.
I don't remember if Zarak ever said where combo receive data is, sadly.