I would think that it depends on the use to which the transcription is being put: if it is a scholarly edition of someone's collected writings then the original version should be used but if the letters are being quoted in a biography aimed at the general public and it is the content that is important then a bit of tidying up to make them more readable should be acceptable as long as there is a note that this is being done. When it comes to punctuation though, it needs to be remembered that styles of punctuation change and that one's own punctuation may seem hideously dated in 50 years time.

Susan