1) Paul was tired because he been working at his report all day long.
Paul was tired - Past Simple
he been working - Past Perfect Continuous
2) First she had breakfast, and then she packed her bag.
she had breakfast - Past Simple
she packed - Past Simple
3) After they had discussed the question for an hour, they came to a mutual decision.
they had discussed - Past Perfect (в данном случае действие "had discussed" в Past Perfect стало причиной того, что произошло другое действие "came" в Past Simple, то есть подчеркивается больше результат действия "had discussed" нежели затраченное время "for an hour")
they came - Past Simple
4) They had been doing their homework for more than an hour and a half when their parents arrived
.
They had been doing - Past Perfect Continuous
their parents arrived - Past Simple
5) The student left the room as soon as he had finished speaking.
The student left the room - Past Simple
he had finished - Past Perfect