Ok, so if you definitely have bad clusters then that could be hindering Autopsy or any other tool from seeing the partition. I don’t know if Autopsy will address the EXT3 partition because Windows requires a separate driver to see it, that’s something I’d punt to the Autopsy people.
You could image the entire drive using FTK imager and then use the Windows to pull it up in Autopsy. This may work but it really depends on what/where those bad cluster are, on weather it will work.
The best thing is to attempt to recover the bad clusters. My goto tool for over ten years is Spinrite (no affiliation) it costs about $90 USD but well worth it. It has saved several of my drives from bad clusters, which made recovery from a non-bootable system. I also use it as a maintenance on all my drives, (twice a year) and I’ve noticed a performance increase on my systems after running it.
You will get the iso or create an iso from the spinrite.exe, make a bootable USB, boot the spinrite (If you have UEFI you may need to set it back to legacy bios/cmos). Run spinrite on level 2 (default) on the drive in question. The down side is expect it to take a long freaking time, days to weeks. When spinrite hits a bad sector it will crunch on that sector until all possible attempts fail, for a long time so no telling how long it will take.