The marks have got to be PDF for Metrix, with attending PNGs for preview. I wasn't real excited about migrating the entire library either, but in the end it turned out to be a good opportunity for some housecleaning. You need to tell Metrix the exact dimension of each mark, so wherever possible I changed them to a semi-even number, and also took the opportunity to establish a new naming scheme, that made more sense than the years-old, random scheme we were using with Preps. In the end it took less than a day. I was able to throw out a lot of old marks, and the ones we still use are now better organized. Making the PNGs is no big deal either: open in Acrobat, save as PNG, done. One drawback is updating marks [which I believe Lithotecnics is working on]: as they are all kept locally, they need to be updated on each machine. We've been using Powerswitch to push out the new set with every update to each station with Metrix. And one further note: Metrix does not support "dupmarks", so we had to make a separate mark for each size and type of colorbar. We had some issues with resaving dupmarks as PDFs for Metrix use, and apparently the extra EPS code that makes them extendible caused issues, so a quick copy-paste to a new document was necessary.
Maybe someone else could comment on Preps-JDF-Metrix functionality, but I still don't think it would be worth the effort, even if it was possible.