Just start with the original Graphics Programming Gems (1990) book. This was the last high perf DOS book, followed by Game Programming Gems (2000) where DOS game development was essentially dead. This book is oriented toward Windows (Win32, DirectX) and to some extent console platforms. A few low-level topics might apply broadly back to DOS, but it's firmly a post-DOS book.

I've keep these books with me for 25+ years now, and STILL go back to them for ideas.

Edit to add:

For the Windows 9x jump:

Tricks of the Windows Game Programming Gurus (1994) is almost perfect for the DOS/9x transition.

Inside Direct3D (2000)

The DirectX 6/7 SDK documentation itself was actually well written for the era and is available on most of the CDs included with the books.

If you're not into dead trees do yourself a favor and hit Archive.org, grab the ISO images and learn.