I have 2 custom factions I like to use that both have "Morgan Yellow"
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Yes changing colour is possible. Just open your customfaction.pcx file and go down to the down-left corner. There you'll see a number of boxes for faction, text, border and vehicle colour. Just copy and paste the Morgan colours to there. The only problem I can't seem to solve with colour editing is that whan I create a custom faction with the Spartan colours, the faction text colour becomes black instead of staying white, even if using the original Spartan pcx file. As a consequence of this you can't see the base sizes.