I’d suggest Stirling PDF, just get the Stirling-PDF.jar
file from the releases. It does really lots of stuff (though I had some issues with creating pdfs with multiple pages per page). It open a port for the service to run locally and once you close it, it also closes the port.
I also use libre office draw (or firefox printing menu) to create pdfs with multiple pages per page.
There’s also xournal as some other people have mention that has some editing capabilities.
Nah, just run chkdsk with any flags you like, this should probably fix it.