That's...extremely strange. I'm able to get to the point you're at, under the same conditions of having a barbaric personality and Mac's romance route, and able to change Killigan's equipment and access the codex without any issue. The problems you're having might be specific to your playthrough.
I'm very sorry to hear that this has been giving you such a hard time, though. There's two things you can try, one of which might restore your save to a usable state. Open up the console by pressing SHIFT + O, input "can_equip = True" and "in_town = True", then input "exit" (all without the quotes). It should allow you to mess with Killigan's equipment and progress, but it may not fix the issue you're having with accessing the codex.
The best thing I can recommend to do is to try making a new save and skip to the closest skip point (the day the group reaches the dreadstone) then catch up from there. It's possible from the other errors you described that something went really wrong with certain important variables at some point, through no fault of your own, and that fucked up the way the game detects when Killigan can mess with his equipment. VERY rarely, the engine "forgets" to do something important during one playthrough and can cause issues like the ones you described.
I'll be combing through and checking to see if anything specific caused the issues you were having and will put out a hotfix ASAP if I find an underlying issue.