I just wanted to follow up with this thread since getting my 650MB discs. It has been night and day in disc read performance between the new discs and what I was using before. Before, the music tracks would drop out or not even load during sequences in Ys IV, and it would sometimes be up to 30 seconds to load a small audible cut scene. Now, the disc loads as if it were a retail disc - the drive is quiet and not always seeking like before, and things load quickly and without fault. In my case, having the right disc has made a world of difference.
My setup is a PE Engine DUO, and the discs I'm using that work great for me are MAM-A Gold Archival 650MB CD-Rs. Before I was using high quality 700MB Taiyo Yudens that were nothing but trouble. To burn the discs I am doing as what was suggested here - ImgBurn at the slowest write speed possible (in my case 4x). Not sure if it is the 650MB vs. 700MB change that is making the difference, the gold discs versus the green-based Yudens, or some combination of the two, but it really has worked. I bought my discs on eBay, but 650MB discs seem to be a hard find these days. Hope this helps someone else, thanks for all your help everyone in this thread.