(1)
Your answer "era pronto" is correct and "sarebbe stato" is wrong.
In "… disse: Sono pronto …" the two actions are simultaneous (he was ready when he talked) and must remain so in the indirect speech: the passato remoto plus imperfetto sequence "Disse che era pronto" expresses this simultaneity.
The passato remoto + condizionale passato sequence "Disse che sarebbe stato pronto" expresses future in the past and would be used, for example in "Appena lasciato l'ufficio le telefonai: mi disse che non sarebbe stata pronta per uscire prima delle 8"; therefore it isn't suitable for your text.
(2)
Here "pagate" in the direct speech becomes "pagavano" in the indirect speech: neither "pagassero" nor "avessero pagato" are correct. This choice of tenses belongs to a very low register.
If, on the other hand, we consider the alternative "se non pagherete" (a far better solution that uses futuro semplice and implies the subject), then the indirect speech changes into "avessero pagato" (maybe the native speaker you refer to instinctively did so). By the way, the most correct way to write this passage as direct speech is arguably "Se non avrete pagato entro i termini che abbiamo fissato, vostro figlio sarà ucciso" but I think that nobody would ever choose such tenses in real life.
Note: the text from your book contains, among other problems, a broken and confusing mix of verb tenses in (1) and the error "Il vostro figlio" (should be "vostro figlio") in (2).