How do I convert 10,000 assorted jpg files to pdf for ocr?

Hi all, my first post here.
Over the years, I've scanned many thousands of documents using various settings and scanners. Now I want to OCR them. I don't have any document imaging system (should I?), I just keep them in folders. I did Acrobat Action to insert a bunch of files and save them as PDFs. This worked, but created a number of problems:
1) it's sloooow
2) I have not checked yet, but I was told it results in image loss? That's the most important part I guess. Any way to wrap my jpg into pdf as is? I was told it can be done programmatically!
3) somewhere in the middle of conversion, Acrobat froze, and now I have thousands of files that have been converted, and thousands more than have not.
I am actually a programmer, but I am under a time crunch and want to do this fast, so while tips and tricks for learning to program Adobe would be very interesting, I just want to get it done at the simplest level possible, for now. I don't care if the process is very slow, as long as it's automated. The one exception is, if there are any command line arguments that could help me, I'd definitely be game (I have cygwin). Or if I get precise instructions.
While I am at it, are there any 3rd party products that do what I want?
Edit: I was told I want to look at DCTDecode filter, but I am very new to Adobe (in fact, this is my second day); how do I do that?

Acrobat isn't designed to process that many files at once, it's designed to be very accurate, so yes it will be slow. OCR is a processor-intensive task even when it's not being done very well.
You may not have a choice other than splitting the files into batches and waiting for Acrobat to finish - normally that many files would be processed with specialist bulk OCR software (which is often bundled with high-volume scanner hardware). As standalone software it tends to be expensive or complex to set up, for example some programs run on a network of Linux servers to distribute the load. If you want accuracy there's no escaping the amount of processing required.

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