Yes JPEG would cause a lot of issues with quality when converting.
Have you tried just making a new PDF from InDesign using File>Export and then print the PDF that it generates?
PDFs can have a massive amount of document overhead - here's a quick guide to looking at PDF document overhead and how to reduce it - it is for written for InDesign files converted to PDFs, but the same principles would apply for the PDF generated from Autocad.
http://indesignsecrets.com/document-overhead-in-indesigns-pdf-can-be-huuuuuuge.php
Try reducing the Autocad PDF document overhead, then place that in InDesign.
Hope that helps.