If I have Mel awakened empowered and I stupefy my own empowered Gangplank, does he only gain 1 might instead of 2 or does he get 6?

Neither — Gangplank gains +3 Might this turn, so he ends at 9 (6 base + 3). Mel's extra −1 never lands.

Empowered Mel makes Stupefy's reduction −2 (to a minimum of 1), but Stupefy chooses Gangplank, so his Empowered replacement fires: a spell that would give him −[S] instead gives him +3 [S] this turn. The entire reduction is replaced — Mel's additional −1 is not applied on top, and the "minimum of 1" floor never comes into play. If you order Mel's modification first you get "would give −2 → replaced by +3"; if you order Gangplank's replacement first, the spell no longer gives −[S], so Mel has nothing to modify — either way it's +3. Stupefy's draw still happens, and the +3 wears off at end of turn. (FAQ #11914; Rule 372.)