Shower needed to be replaced it was 40 years old and glass cracked... the new seemless shower did not line up with the original holes and I am afraid that the caulk will look horrible to try and cover the
Holes any suggestions...

Lets see if I have it right. You have install a one piece shower enclosure over existing wall finish. The front edge does not come out as far as where old shower door was mounted and the old ho;es are not covered by new door frame.

If possible replace tile with holes. You can use tile from behind enclosure if not installed yet or buy new at a big box store.

If you can show a picture may be able to help more.

Chuck

Holes never lined up, especially on 40 years old shower door. Grout the old holes. That will prevent water from entering your wall.

Hope that helps

Milo