All of your versions work. Hmmm. Is the subject supposed to be part of the question?
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AvangiDid you pay the second night yet?Hmm. the second night and the room don't do it for me at all (nada, zero, zilch), though rent, bill, mortgage, and ticket (and check, tab, and tax(es)) sound fine as perhaps a fourth form.
Did you pay the room/rent/bill/mortgage?
CalifJim They sound as weird to me as Did you drink the room?Perhaps it only seemedas if I did.