The usage of ghost has changed over time. There was no confusion 400 years ago though.
Holy Spirit
(or Holy Ghost)
• noun (in Christianity) the third person of the Trinity; God as spiritually active in the world.
http://www.askoxford.com/concise_oed/holyspirit?view=uk
ghost
• noun 1 an apparition of a dead person which is believed to appear to the living. 2 a faint trace: the ghost of a smile. 3 a faint secondary image produced by a fault in an optical system or on a cathode ray screen.
• verb act as ghost writer of.
— PHRASES give up the ghost die or stop functioning.
— ORIGIN
Old English, "spirit, soul".
http://www.askoxford.com/concise_oed/ghost?view=uk
spirit
• noun 1 a person’s non-physical being, composed of their character and emotions. 2 this regarded as surviving after the death of the body, often manifested as a ghost. 3
a supernatural being. 4 the prevailing or typical character, quality, or mood: the nation’s egalitarian spirit. 5 (spirits) a person’s mood. 6 courage, energy, and determination. 7 the real meaning or intention of something as opposed to its strict verbal interpretation. 8 chiefly Brit. strong distilled liquor such as rum. 9 a volatile liquid, especially a fuel, prepared by distillation.
• verb (spirited, spiriting) (spirit away) convey rapidly and secretly.
— PHRASES
in spirit in thought or intention though not physically. when the spirit moves someone when someone feels inclined to do something.
— ORIGIN Latin spiritus ‘breath, spirit’, from spirare ‘breathe’.