I gave up on trying to understand what Google wants. Same thing happened to me, hundreds of pages and products were not indexed anymore. I did everything possible with no change. I left the site alone and 2 months later everything was indexed and back to normal. 4 days later they took it all away again. This is with me doing nothing at all.
Sounds like you have a lot of work, are those unrelated pages still on your website? that could be a factor, as well good mentioned that it could take months as they re-evaluate the site and see where your website fits in.
I had a client site also hit and we also added a lot of relevant content aggressively.