Thanks for the reply, especially regarding the ill-matching between 'by' and 'still'.

One unexpected thing in your explanation, though, was that you don't seem to care much about whether I used past perfect tense or simple past in the main clause after "by then" and "by the time she arrived". After all, you saw that No.5 sentence is 'correct', but No.1 needs improvement, which makes me dumbfounded.

I thought No.5 sentence is only a informal variation of No. 1, which shows past perfect tense after "by then".

If you compare these two sentences only, which do you prefer to be more grammarically correct?