it's better to post a small reproducible example - running the whole code you provided requires installing packages and diving into your code's logic - which usually makes it a lot harder for people to assist :)
i didn't end up running the app, but from examining your code i see two issues:
1. in your ui.R file, at the commented-out line 46, you have columns which are not wrapped in a fluidRow (the ones inside the box) - this can cause display/alignment issues.
2. in your server.R file, when rendering a valueBox you're not using the 'color' argument.