What is the right way to express pH and concentrations?
This is more a question of English usage than Chemistry, but the English Language and Usage people regarded it as “proof reading” and migrated it here. So I will move my original comment here to make it an answer (until the Chemists throw the question out).

First, you really should try to answer this yourself by looking at the style used in scientific journals relevant to your work in papers from English-speaking countries with authors whose surnames suggest they may be native speakers. Several of your alternatives are grammatically correct but unneccessarily long-winded and never used.

Having said that, my opinion (as a native English-speaking biochemist with many publications) is:

A: A-1 (“a solution of pH 3”) should be used. 

The use of ‘with’ alone in A-2 is unusual, A-3 is ok in speech but too verbose for a paper, A-4 with two ‘of’s is clumsy, ugly and unnecesary.

B: B-1 (“a 3 nM buffer solution”) seems best to me — brief and correct. 

There is no need to expand it as in B-2, B-3 (both of which sound clumsy and I advise you not to use), or B-4. B-5 has the ugly double ‘of’ again. 

If for some reason you don’t like B-1 you can name the buffer in a phrase such as “3 nM Tris-HCl Buffer”.