Your high level perks mod is very nice, though I think some of the effects are a bit too OP (run speed bonus from Cardio, for example). However, there is an issue with the recipes part, where it removes the scaling cost of weapons that are crafted at workbench (instead weapons cost less the higher level you can craft them at). I'm assuming this is unintended.
Something like that to fix it, maybe:
/recipes/recipe[@craft_area='workbench' and contains(@tags, 'perkAdvancedEngineering')]/effect_group/passive_effect[@name='CraftingIngredientCount']/@level
Additionally, it might be better for compatibility with other mods to change xpaths for Advanced Engineering crafting unlocks to contains instead of =, this way if a mod loaded earlier adds a recipe, your change won't fail to apply.
I think there might be an issue with reducing crafting costs (instead of reducing the base and giving lower levels a percentage increase), where the game wouldn't let me craft the max number of stuff I theoretically had resources for (eg. by pressing the max button in crafting). The issue disappeared once I removed the percentage reduction at later levels.
I also think that crafting time reductions from Advanced Engineering don't seem to work, but I have no idea why (I had lvl 8, someone witth a lower level could craft ammo and steel faster). When looking at the xml, everything seemed fine. I solved this by adding more separate CraftingTime passive_effect for higher levels:
<append xpath="/progression/perks/perk[@name='perkAdvancedEngineering']/effect_group" >
<passive_effect name="CraftingTime" operation="perc_add" level="3,8" value="-0.2" tags="forgeCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="4,8" value="-0.2" tags="workbenchCrafting,cementMixerCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="6,8" value="-0.35" tags="forgeCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="7,8" value="-0.35" tags="workbenchCrafting,cementMixerCrafting"/>
</append>
Now that I'm writing this, I could have just tested something like that instead:
<append xpath="/progression/perks/perk[@name='perkAdvancedEngineering']/effect_group" >
<passive_effect name="CraftingTime" operation="perc_add" level="3" value="-0.4" tags="forgeCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="4" value="-0.4" tags="workbenchCrafting,cementMixerCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="6" value="-0.6" tags="forgeCrafting"/>
<passive_effect name="CraftingTime" operation="perc_add" level="7" value="-0.6" tags="workbenchCrafting,cementMixerCrafting"/>
</append>
But my edit worked well enough.
In general, this mod is a bit troublesome, compatibility wise, since most other mods set their unlocks to eg. levels 3,5, but I'm not sure how this could be fixed. Adding those as separate perks that would stack with base ones could help (you'd still have the 5th lvl perk for other mods), I think you could base_add the CraftingTier, but there might be some issues with this approach I'm not seeing.