It's precisely those idiosyncrasies of early modern orthography which make it difficult to use an off-the-shelf OCR package, which is presumably why these are hand-transcribed instead.
Perhaps there is a specialist antiquarian OCR package which can deal with long s, interchangeable u and v, non-standardised spelling, etc, but I have yet to come across one.
Have you looked at The Early Modern OCR project? My understanding is that they're working on exactly that as well as simply better tools for reviewing & retraining on a large scale:
Perhaps there is a specialist antiquarian OCR package which can deal with long s, interchangeable u and v, non-standardised spelling, etc, but I have yet to come across one.