I readjusted the interpupillary distance and the diopter and it seems to have helped some.
Yes, adjusting the interpupillary distance is important to get strain-free stereo vision. It may take some time to get it just right for you.
It is possible(likely?) that some of the headache/discomfort is from muscle/neck strain.
You may need to adjust the height of the table (easy to put a block under the microscope, not so easy to lower it) to get just the right height for comfortable viewing. Just an inch or two difference can make it MUCH better (or worse).
After spending some more time with the scope, I suspect that the better part of the headache is from the bright light.
I have blue eyes, and am pretty sensitive to light. I wear sunglasses outside most of the time--when the sun is bright. Along with the microscope, I bought the 144 LED light ring
144 LEDS?? YIKES! I have a homemade 8 LED ring and it is a bit glaring. These LEDs are only running about 10 mA each.
See if you can put a dimmer on that thing!
Jon