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Your best bet would probably be to look into the Onyx M90, the Sony PRS-950 (on sale at Best Buy for $200) or the Kindle DX. The M90 and DX have 9.7 inch screens. The Kindle has some pre-set zoom settings, but other than that is lacking in PDF functionality (it has problems with tables of contents, for example). The Sony PRS-950 is a smaller device (7 inches), but it can handle PDFs well and would probably be good for reading PDFs with columns, as it has a custom zoom for PDFs with two or three columns. It can also reflow PDFs and zoom. You can also try using a program like Briss (it is free software) to cut the margins on your PDFs or divide the page into smaller sections to make it more easily readable on a smaller screen.
A large screen e-ink device should be fine for your needs, I think, especially if you pre-cut the margins with Briss or a similar program. Figures and equations should be fine in PDFs. I've read scanned PDFs and PDFs with foreign, embedded fonts with no problem on my Sony reader, so I don't think that you should have a problem with equations. Hopefully someone with a bit more experience will be able to comment further on the rendering of equations. The main problem with PDFs and e-ink is the small screen size and relatively slow page turns, which are fine for reading linear text but can be a hassle when trying to jump around in a text.
You can also look into the Entourage Edge and Pocketbook 901 or 902. The M90 looks like a really good device to me, but it is brand new so I haven't read too many reviews yet.
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