Armor and Weapons
Source GM Core pg. 135
Specific armor and weapons have a minimum grade and varying number of upgrade slots, so you have a lot of space to design. Choose abilities that feel attached to the fact that they're weapons or armor; for instance, a painglaive with extra-long teeth that you point at an enemy to launch bits of steel is more on theme than one that casts wall of steel in an unconnected way.
The specific item should cost more than the base grade armor or weapon would with just basic weapon and armor upgrades, but you can often discount the cost of the additional components significantly as part of the specific item's special niche. Be careful about specific armor or weapons that include weapon upgrades in addition to unique specific abilities. If you discount the item, you might end up with an item significantly superior to one built using the normal weapon upgrades system. That's not always bad since it's still giving up customization for power, and this can be appropriate if the item has an important place in your story. Just make sure the difference isn't too drastic. If you just want to create armor or a weapon with upgrades and no extra special abilities, you can do so. The Price of such an item is the sum of all the upgrades' Prices, and its level is that of the highest-level weapon upgrade on the item (if higher than the grade of the weapon).
The specific item should cost more than the base grade armor or weapon would with just basic weapon and armor upgrades, but you can often discount the cost of the additional components significantly as part of the specific item's special niche. Be careful about specific armor or weapons that include weapon upgrades in addition to unique specific abilities. If you discount the item, you might end up with an item significantly superior to one built using the normal weapon upgrades system. That's not always bad since it's still giving up customization for power, and this can be appropriate if the item has an important place in your story. Just make sure the difference isn't too drastic. If you just want to create armor or a weapon with upgrades and no extra special abilities, you can do so. The Price of such an item is the sum of all the upgrades' Prices, and its level is that of the highest-level weapon upgrade on the item (if higher than the grade of the weapon).
Runes & Upgrades
Source GM Core pg. 136
Runes and upgrades should never be on the same weapon. Runes (including spells and effects that confer runes) only function on archaic weapons, like those found in Pathfinder. Upgrades (including spells and effects that use upgrade slots) only function on weapons with the analog or tech traits. There are some explicit exceptions, such as hardlight handwraps, but if those items have upgrade slots, they should never have runes (and vice versa).