Or should the comma come before the question mark and hence 'he' will start with a capital letter. -- No.  See above.  If it is correct, is it always true that commas follow the question mark and not vice versa?-- No.  See above

When at school I was sure that there was a rule with commas that they didn't come before 'and' or 'because', e.g., it seems to have drained him and created a bout of "severe cramp," because he was unable to complete the match.-- A comma precedes 'and' when it is a conjunction between 2 independent clauses and sometimes when 'and' precedes the last item in a list.  Otherwise, it is omitted.  Commas before 'because' are used if the clause seems non-restrictive but are omitted if the clause seems restrictive.

P.S. We all know that school rhymes are not always true, as in "I before E except after C". I think I could name about ten off the top of my head where this isn't true, e.g., weird, vein, etc. etc.-- Good for you.

"Is that you, Susan?" he asked the maid downstairs.

There are two 'rules' involved here.  (1) The punctuation within the quoation marks belongs to the quote or utterance and is not a punctuation of the overall sentence.  (2) Quotations are set off by the introductory or other text (He said; said he) with quotation marks alone; any other punctuation is redundant or obfuscatory.