I'm careful when doing the actual capping part and haven't caused myself any pain while doing it, only tiredness and if one arm gets too tired, I'll switch it up for a while. I've also since manged to rig it to make the caps without using the mouse at all and instead use the 0 key on the number pad and can easily alternate which finger I use to push the button. Mostly it's just a time-consuming tedious job. I do end up getting pretty pictures at the end though.
My next sceencapping job won't be until at least January, so I'll have had about a six month break by then. The other parts of the job I do for the site aren't so bad.
