50 caps for a fix and 100 for a rad cleanup is a bit cheap. I was wondering, is there a way to increase the doc fee globally?

Those are handled in the quests... try looking at VDoctors quest, you will see various "DoctorMedicalXX" topics. In each of the "goodbye" topics, you will see a line in the Result Script edit box like:

player.RemoveItem Caps001 100

You would need to go through and change all those. You could probably setup a global variable for your mod and then replace the 100/50/etc with that variable in all those locations so that you could change it on the fly based on Karma or something.