I also have some comment son the non-magical item enhancements

Why is the system so complex?
- Why require multiple skills? Items using this system require the regular craft skill and also craft traps, making it more difficult for characters who rely on skill ranks to be good at it.
- Why the extra stages to the process, first crafting the slots one at a time, and then crafting the modifiers? Magical items don't need multiple stages.
- Why have an extra % cost for modifiers to magic items? Magic item creation doesn't require this kind of calculation.
- why does this crafting take so long?
With a +40 skill modifier and taking 10 (and assuming the craft DCs can be upped to exactly 50 for convenience of calculation), a crafter can produce 250gp of work per week.
This means, for example, a Breakthrough 5 weapon will take 260 weeks to craft.
For comparison, a spellcaster can craft up to 14000gp of magic items per week, and can have an assistant double that rate with the right feat (and that's before any boosts from the tool enhancements in this document).
- Why have each slot hold one minor and one major modifier? Is there some reason that items shouldn't have more than 5 minor modifiers? Should polished durable arrows really require cost more than +1 arrows?


The whole system would be a lot simpler if it worked like magical item enhancements - but able to be done by non-magic-users.
- Just price everything as if it was a magical enhancement (either a +X modifier or a fixed price), that way the costs fit in with magic enhancements. That would also make benchmarking the costs against magic far simpler.
- Put some rules in place for which characters can do the crafting. I would suggest skill rank requirements for individual enhancements, just like magical enhancements have spell requirements. To make this function like crafting feats there would need to be no option to up the DC to ignore the requirement. The skill required could even vary depending on the enhancement.
- If the goal is for mundane crafters to be unable to keep on adding properties to an item endlessly - then set a scaling DC for the crafting based on how much (or how many) non-magical properties the item already has.

That would be far simpler overall.