Hello @sstrzesynski
If all the parts in your project are custom symbols, they will appear pink in the project otherwise they are not colored in.
Creating a custom symbol in Scheme-it - DigiKey TechForum
For the wire color when you select it you should be able to change the color on the right-hand side of the screen when you left click the wire once, see the screen shot below.
As for the issue you are having with saving the project, I have reached out to our team, to look into this error.