And somewhat OT, but a good copy is also just a $5.99 problem 100% legit at Gog.com: http://www.gog.com/game/ultima_456 - but not a help if you are trying to archive real images for your project, I know. 😀
However, back on topic, I haven't had any luck in years getting good quality IBM disk reads myself, but I mostly stopped trying. I like my FC5025, though it's gathering dust, and I look with curiosity on the “Catweasel mk4 Plus” and the KryoFlux ( http://www.softpres.org/glossary:kryoflux ) but I haven't tried them.
Back in the day, the best diagnostic tools I found were the Ultra Utilities that were able to detect, report, and imitate/duplicate many of the funny sector copy protections. I've got a copy, and think I've found them around the net, though the name is common enough to not be disk utilities sometimes. I'll try to dig them up. But some games copyprot (no idea about ultima) required custom hardware to do things real drives couldn't, and I didn't use any of the super cracking disk duplicator tools out there - some of those were supposed to be good. And of course, your funny sectors could just be degraded disks, not copy protection schemes, as you say. Sorry, no idea.
Here's a fun link on the topic I hadn't seen before: http://archiveteam.org/index.php?title=Rescuing_Floppy_Disks