That's great you got it sorted but I'd thought I'd share what I changed and have been using on your previous upload.
<configs>
<!-- HARVESTING_TOOL_SKILLS -->
<set xpath="/progression/crafting_skills/crafting_skill[@name='craftingHarvestingTools']/effect_group/passive_effect[5][@name='CraftingTier' and @value='1,2,3,4,4']/@value">1,2,3,4,5</set>
<set xpath="/progression/crafting_skills/crafting_skill[@name='craftingHarvestingTools']/effect_group/passive_effect[6][@name='CraftingTier' and @value='1,2,3,4,4']/@value">1,2,3,4,5</set>
<set xpath="/progression/crafting_skills/crafting_skill[@name='craftingHarvestingTools']/effect_group/passive_effect[7][@name='CraftingTier' and @value='1,2,3,4,4']/@value">1,2,3,4,5</set>
<set xpath="/progression/crafting_skills/crafting_skill[@name='craftingHarvestingTools']/effect_group/passive_effect[8][@name='CraftingTier' and @value='1,2,3,4']/@value">2,3,4,5</set>