There are myriad square tapered cranks out there on the used market- awesome ones too like RF turbines, Kookas, White Inds., and many many more. But if you do want to modernize, ISIS would be the way of the future as far as crank/BB availability is concerned.
If it were my frame, I would build it as light as possible. Ti just screams for lightness and strongness; 2.5lb '02 SID race, carbon bars here, Thomson stem there. XT front, XTR rear, XT pods, Avid Mag brakes w/ Ti. levers, Chris King everywhere...oh man, I want to build a Ti bike.