The only Latin word I can think of that uses the letter Y is Myrmillo, which refers to a type of gladiator which wore a heavy helmet with a high crest and broad rim that resembled a fish. The name for the gladiator was first coined in Latin, but is derived from on a term for a saltwater fish which had been borrowed from Greek. There were alternate spellings for the gladiatorial term using the letters U or I instead of Y, and the fish itself was often spelled with an O instead of an Y.
Originally, the letter C made the G sound, as it was borrowed from Gamma. Over time the pronunciation of the letter C shifted and displaced the letter K (previously derived from Kappa). The letter K continued to be used the in native Latin word Kalendae (the first day of the month) and sometimes its derivatives like Kalendaria (Calendar), but was normally reserved for when one wanted to make a word seem foreign (usually something borrowed directly from Greek). RVCA, the first man recorded as opening an elementary school, insisted that his name be pronounced the old fashioned way and so invented the letter G to made the distinction clear. (Alright, modern scholarship largely rejects this, claiming the letter was in use already before his lifetime, but ancient authors certainly gave his the credit.) He assigned the letter its place in alphabetical order, replacing the letter Z, which had been borrowed from the Greek Zeta long before but was never really used in Latin. Once Latin writers started using more and more Greek words the letter Z was reintroduced, and placed at the end since g was firmly entrenched. By that time the letter Y had already been introduced to denote the "Greek I" sound.