Either 1: Find a font with small caps (with small cap figures) notably taller than the lowercase, or 2: Use regular capitals. If the units are supposed to go in text, I'd probably keep the numeral style from the rest of the content. Lowercase numerals make more sense in a mixed case setting than with small caps, anyway.

Looking at frode frank's suggestion from the other point of view, you could use a font where the capital letters (and regular numbers) are smaller than the full height. Gentium is a free one. Greta Text is an expensive one.
http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&item_id=Gentium
http://www.typotheque.com/fonts/greta_text/

Myself, I think the standard numbers and letters would be fine.

Whatever you do, make sure you're not getting too far away from the standard for your business or field of study. If in doubt, stay close to the work of other people. Sometimes un-fancy is best.

A remark unrelated to your post... Man, that Arno Pro really looks good in your PDF. That's a nice font.

Sometimes un-fancy is best.

I want to second that. I had a probably similar case: a scientific treatise with figures happen which to appear in many different roles: dates, numbers, tact figures … a lot more.
There comes the point when you realize that you could find a fancy solution for each special case. But altogether, it won’t be convincing to mix half a dozen fancies into one typography. What I ended up with: lining figures and that’s it. The figures of the font should be decent, of course.
Less is more, sometimes. Maybe simple is best.

Fancy is for dandies.
Simple is for simpletons.

Shoot for the third option.

hhp