Okay, so after threating to throw my teddy in the corner (not that I would do such a mean thing) I have fixed my problem. I properly added the 30.06 caliber from CaliberX so now it activates properly, and there are no more errors in FNVEdit. It still bugs me that these errors occurred. My only guess is that I messed up when saving the Dead Money plugin, as this moved it out of the Data folder and into MO's overwrite folder, so I'm guessing this messed up the references some how? Whether this is the case or not, I'm only going to make changes to one plugin at a time from now on, and I've benefitted greatly from making backups and even backup-changelogs!
Thankyou for all your help! (Yes, I know there are no replies, but I could feel the good-will of this community guiding my paws to the right path.)
I've found a simple solution: selecting 'Toggle 1' to [1] in the ingame menu reverts IS zoom to vanilla values, so if I change the Sight FOV in FNVEdit for each weapon individually I can set the amount of zoom. In this case, my FOV is 75, so I set all weapons to 75 too, while leaving the problematic weapons at their default FOV. Problem solved!
ToughPuppy's post in Please help me in my modding endeavours! was marked as the answer