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Fly after having left for day in harbour(4)-E-L looks pretty certain

very tenuous but....

heel(follow close behind) - heed(very vague connection to harbour as in a grudge) with l for d

Not "very" tenuous - I like it, but...
the third letter of 28d is the second letter in 31a Pay upfront for unlimited cereal crop(A--E); ie if it were 'heel', 31a would become AE-E! By the way, I thought of 'ANTE' for 31a, but can't reconcile this with the rest of the clue.

not doing the crossword but looks like ae?e rules out my stab

The word is HERL - one of those Chambers words which directs you then to HARL, and one of its meanings is fishing fly

I forgot to give the wordplay:- one of the meanings Chambers gives for "herd" is harbour - and so change the "D" for "L"

think the other one is "arle" - barley without by

Many thanks AJT and ixion