Whenever I print it there are all kinds of random errors at random points depending which program I use (even Acrobat won't touch it, and it created it).
Are the errors when printing direct to a printer or RIP (what type of printer, RIP etc) or to a PostScript file?
Have you tried printing in batches of smaller amounts of pages, say 10x100?
I used to get "binder" files from clients that would have some pages that were OK, other pages would have errors when printing. As Lukas states, this is usually due to the original PDF files not being of consistent quality before they were combined in say Acrobat Pro. As a last resort the problem pages sometimes had to be printed from Acrobat Pro "as image" (600 ppi or higher) rather than as PostScript. The print as image command is "sticky" and one has to remember to turn it off again after it is used (not the best option).
Can I convert it to an error-free pdf?
Try to do a save as from acrobat to PDF, which can remove junk and reduce file size.
Try to do a "PDF Optimizer" step from Acrobat, selecting the various settings as desired to simplify the file (this will likely take a long time).
Try to use Acrobat Pro to save as .ps or to export to .ps or .eps (transparency will of course be flattened). Then distill the .ps/.eps to PDF. This could be done from the 1000 page PDF, however you may have better luck doing this from the original PDF files before recreating and recombining the refried PDF files.
Yes, this can take a lot of time.
There are of course many other non Adobe PDF options out there. As you mentioned, using say Apple Preview or Apple Automator will likely reduce the quality of the PDF files. Other options that could be explored include:
Document management, PDF reader, PDF creator, PDF editor
gDoc Creator
Nitro PDF Software — Create & Edit PDF Files
PDF Split and Merge
Merge PDF files. Free download. [A-PDF.com]
Adolix Split Merge PDF - free pdf combine, append pdf freeware, split pdf files
(and more by using appropriate web search keywords)
Regards,
Stephen Marsh