This is weird, soulfire is a starting ability for all psi ops in LWOTC and should be immediatly available after training. Since you also cannot equip Psi amps something must be broken, so you are not missing anything.

My first guess would also be a mod conflict issue, logically speaking it should be a mod that influences how psi ops work, but it could also be a mod that changes something about secondary weapons or psi amps in generell. It might be worth noting that not all mods can just be disabled mid-campaign. You can try to check the mod page if something about this is listed there, although this is not always the case.

To your reaper issue: Reapers cannot equip claymores anymore, their new secondary weapon is the throwing knive, unfortunatly I didn't pick the claymore perk for one of my reapers, so I cannot tell if this changes once you unlock the perk.

EDIT:
You could try to clear your config files. I posted how to do so in this thread: https://steamcommunity.yuanyoumao.com/workshop/filedetails/discussion/2683996590/3187992337824741256/
or you could go straight to the original post by Twinux: https://steamcommunity.yuanyoumao.com/workshop/filedetails/discussion/2683996590/3189113164077160590/