Besides an extra cylinder, your CB350 had higher compression, probably larger-area valves (than a KLR650), a camshaft with higher lift/duration/overlap than the KLR's, and . . . quite possibly, a 180-degree crankshaft (insuring a constant air-volume crankcase, not pumping in and out whole displacement with each crankshaft revolution, as does a single-cylinder engine). Add to that, the higher rpm (as pdwestman says). So . . . the CB350 can process more fuel per unit time than a KLR650, cc of displacement to cc of displacement.
Not that a single can't develop horsepower; KTM690 (with only 690 cc displacement) produces nearly 70 maximum horsepower (maybe, measured at the crankshaft, not the rear wheel).
“You better put down that gun. You got two ways to go, put it down or use it. Even if you tie me, you’re gonna be dead.” "John Russell" (Paul Newman), Hombre