Make sure you move your capital and move it back to get the distance to capital modifiers to kick in properly. The values you're talking about sound more like what you get in Timbuktu when you've loaded the game and not done that.
Evil, EVIL bug that knocks my 5000 florins per turn merchant income down to like 1000 at most whenever I forget about it after a reload.
I think skill gain is less about length of time spent on a resource and more about how many florins the merchant has processed. As in, you gain skill faster sitting on a 100 a turn resource than a 10 a turn resource.
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