So I am currently using a 1.12 version of this game for another program to work. The runes are white though. DO they get orange in 1.13 earliest or is it something else. And, can I upgrade the game w/o eliminating the set up?

yep, 1.13:
https://www.theamazonbasin.com/wiki/index.php/Patch

there's a mod that colors runes red for <1.13. look for RRM:
https://www.diabloii.net/forums/threads/game-changes-help-thread-inc-atma-gomule.849306/