Hi,
if you have a look at the source code, under the directory blocks, you can find the code for the different standard blocks.
In each of the js files there is a constant with the color of a category.
For example in math.js you can see the line:
Blockly.Blocks.math.HUE = 230;
You need to change that value, but you don't need to change the Blockly source code for that.
You can just change that value in your javascript before injecting the workspace.
The same goes for the other categories, just look for the corresponding .HUE constants in each of those js files.
Best Regards,
Miguel