I understand you test with only 4 threads and that's of course a problem to play 1000 games. But you can increase that number. Edit 'start.bat' -
ccc -concurrency 4
ccc -concurrency 8
And things go twice as fast in case your PC has 8 threads.
Secondly, start with 100 games. What counts are the suspect cases reported in the 'book-remarks.txt' file.
Thirdly, and this is an overall answer (advice) also on your PM. It's impossible to create the perfect book solely based on computer analysis because of the human preference for openings. There always has to be the 'final touch' by the human hand based on his likes and dislikes for opening theory.
What is possible is to take out blunders and suspect moves based on computer scores. The ProDeo Book Testing is just one of the possibilities, POLY offers you more, IMO the [F5] function is the best, see - http://rebel13.nl/text/result.txt
With all these informations manually tune your books with SCID and re-run the match for a better result. It's the way Jeroen Noomen created the strong REBEL books in the 80's and 90's, the final human touch.
Another way is to create opening books from eng-eng matches between 2 strong engines. There likely are no blunders. The disadvantage is that books lack variation but if that's no problem for you try that path.