Thank you so much, it seems to work now!
Now how did that get there? 0.o I must have had way too many windows open and copied it to the wrong place lol. I know better than to have 2 copies of module manager or put mods in random folders haha. Although I am still getting a similar error about duplicate names, but now instead of there being 2 lines for each error message there is only 1, but the mod seems to work now. I suspect somewhere I have another copy hiding.
I did go through all of my other folders to check that there wasn't anything obvious now, and I didn't find anything else. I should only have universalstorage2, but if my log file says differently that would be interesting. I was hoping that removing the copy of MM would also fix my reactors not being controllable but that's not the case.
Edit: After doing some more exploring it seems that the kerbalism config file for near future reactors was overwriting the control system. Strange, I wouldn't have expected it to change how they operated... oh well, it seems to work for now... unless I broke something else deleting that config haha. Thanks for the tip about the plugins!