If using The Book of Manor, are the Winter Phase raiding/pillaging modifiers in the Great Pendragon Campaign still applicable? I ask this because the Weather roll in the GPC uses d20 and The Book of Manor uses 3d6+5.

my advice would be to use the raiding/pillaging rules from pg.41 Book of the manor instead of the gpc raiding rules, not that there is much difference the Book of the manors is just a little nastier.

Book of the manor raiding rules GPC Raiding rules
Raid +1D6 Raid +1D6
Plundered +1D6+6 Plundered +2D6
Pillaged +2D6+6 Pillaged +3D6

That would be my advice as well. If you are using BotM, use its modifiers rather than GPC's.