it seems like I can't upgrade the various weapons even though i have them in my inventory. IE: I build a bolt caster and try to upgrade yet it says i'm missing one bolt caster to upgrade to the magnetic one. it also seems like it doesn't fully copy all the research options. For example, i couldn't research a hunters axe even though i had it. The research option never appeared and I wasn't able to research it to make more.

in a recent playthrough, the bolt caster option was removed and when i upgraded to the arc blade, the ionic axe was nowhere to be found.

I was able to research everything, but like you, I have an item in inventory, not equipped on anyone, yet when I go to build the next tier weapon, it says I don't have that weapon, even though, clearly, on the same page, I do.

I don't know if conflicts are happening because of other class mods or not, but the best I could manage was building a couple of the powered shadowkeepers, a copule enhanced shadowkeepers, and my best luck was with ionic axe and fusion axe. For a while I couldn't build either of those, and somehow later on, had enough to build them even though it wasn't synching up to what it said I needed to make them.

Its strange, I couldn't buld them, then I could, and I could make a lot of just the fusion axes. I do like the concept of this mod and its a great idea when you're modding in larger squad sizes and enemy pods. I hope someone gets another whack at this.

I have a similar problem, where I can build multiple bolt casters, but can only upgrade one of them to magnetic, and plasma.