Should I confirm pins not located just below the first letter of the text?
Use your judgement on this one. If the pins are sufficiently close to the text to be clear they are associated with it please do confirm them. After all the pins indicate the point on the map where the text appears rather than the exact location of the feature being described. If the pins are some way off from the text and not clearly associated with it please create new pins in the correct location beneath the first letter of the text and do not confirm the existing wrong ones.
Once all transcription is done we intend to do some data cleaning, including purging the unconfirmed pins from the final gazetteer.