At desktop resolution, the floating table of contents menu blocks out two of the (excellent) illustrations (second and second-last). Deleting aside.toc was very helpful.
Yes, I would suggest increasing z-index on images so they pass above the toc. Adding a large dropshadow to the images the same color as the background would make it look like it fades out as it passes by. That's what I did for our blog that has a similar floating TOC + images that escape the text width.