@jjbones123 Please don't quote whole posts to indicate who you are replying to, it makes scrolling down the page slow and is especially difficult for people who are accessing this on their phone. If you want to make it clear who you are answering, just use the @username convention as I have done on this post.
You didn't mention in your OP that you were using a script. I am guessing that the Yanfly script you are referring to is the Ace Core Engine script. That overwrites the default scripts in a number of places, including font colour. If you want to keep that script (and it does a lot more than just affect the text), then you can change the colour there. The section is this, starting at around line 234:
# - System Text Colours -
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
# Sometimes the system text colours are boring as just orange for HP, blue
# for MP, and green for TP. Change the values here. Each number corresponds
# to the colour index of the Window.png skin found in Graphics\System.
#=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
COLOURS ={
# :text => ID
:normal => 0, # Default: 0
:system => 16, # Default: 16
:crisis => 17, # Default: 17
:knockout => 18, # Default: 18
:gauge_back => 19, # Default: 19
:hp_gauge1 => 28, # Default: 20
:hp_gauge2 => 29, # Default: 21
:mp_gauge1 => 22, # Default: 22
:mp_gauge2 => 23, # Default: 23
:mp_cost => 23, # Default: 23

ower_up => 24, # Default: 24

ower_down => 25, # Default: 25
:tp_gauge1 => 10, # Default: 28
:tp_gauge2 => 2, # Default: 29
:tp_cost => 2, # Default: 29
} # Do not remove this.
You can change the colour 0 in the same way as Rinobi suggested.