I think some issues are being missed here. The Amazon Kindle software would be a direct scan into the Kindle format. It should go real well and be nice and clean.
Those reviews of the Kindle software are from people trying to convert existing PDF files they already have into the Kindle format. And obviously it is not working very well.
Now if you go to the free software people are recommending (Calibre) and read a little bit you will see that they say PDF is about the worst possible format for their software to attempt to convert to something else. It is about number 15 on their list of preferred formats to convert. So it is no wonder that Kindle also has a problem trying to convert PDFs.
I think for somebody with old books available only in hard copy the Kindle app might work quite well to get it into electronic format.
Obviously lots of pamphlets and newer guide books these days are available as electronic but for those precious older guide books that we might have the Kindle app or perhaps some free app may do the job for you.