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Hammer of wrath says you score an autohit at your base strength when you assault. Does this still use the stats of your weapon? IE, bonuses to strength and any special abilities/AP it has?

Base strength = base strength.

Weapons modify strength (and other attack characteristics).

Modified strength =/= base strength.

Therefore, the answer is no.

The HoW rule is quite clear on what the characteristics of the attack are.

It is even clarified in the FAQ, to say no special rules at all.

Just as a slight caveat look at the DE FAQ... apparently no wargear isn't quite true. PG 4 lower right side.