Captain Beefheart had been friends with Zappa since they were teenagers, and appeared on the album Bongo Fury (and was on that tour as well). The two were rivals as well as friends, and eventually they got pissy with each other and remained out of contact until near the end of Zappa's life.
When I tried to think of a way to connect the name "Captain Beefheart" to gaming, my first reaction was PIRATE MINOTAUR!
I should have had more faith in the powers of the Internetz to provide what was needed, because:
Captain Beefheart (NPC)--The notorious pirate is the offspring of the Minotaur of Crete and the Queen of Pirates. He was raised aboard his mother's ship Wings of Vengeance, and assumed command upon her retirement. He is a brutal foe and a devoted son, and hopes to make his mother proud by becoming the richest and most renowned pirate of the age. He is immensely strong and, in addition to a fine scimitar, carries a unique three-barreled flintlock pistol he calls "Hambone."
Init +0; Atk scimitar +6 melee (1d8+5) flintlock pistol +4 missile (1d6+2) or Charge +5 melee (1d6) and opponent must make Reflex Save or be knocked prone; AC 13; HD 5d10 (30 hp); MV 30’; Act 2d20; SV Fort +5, Ref +0, Will +4; SP: Strong like bull; Charge! AL C.