"Rite" is God's established form, manner, method of expressing, implementing God's, Covenants, Commandments.

"Rites" are the initial forms of the fulfillment of God's Commandments which contributed to the realization and correction of man's sinful character. 

Negative Meaning.

"Rite" is the ritualized, bootstrapped, formal fulfillment of God's, Covenants, Commandments.

"Custom" is an established, fixed in the minds of the people sinful secular, false religious patterns, rituals, which are an evasion from the knowledge of God's Will, from the fulfillment of His Commandments, Precepts.

"Customs" are religious traditions based only on the "Letter" of the Scriptures, but not on their Spirit.