(2) She had entered the room and found him laid on the floor with the box in his right hand.
You describe this as "the past perfect and the simple past", but in fact it will not be parsed this way. Found is both the simple past and the past participle of find, and in this case it will be understood as a past participle: both are governed by the perfect auxiliary had. In effect you have two past perfects.
She had entered the room
and found him laid . . .
(3) She entered the room and found him laid on the floor with the box in his right hand.
In this case, where there is no perfect auxiliary, both entered and found will be understood as simple pasts.
She entered the room
and found him laid . . .
Either of these is formally acceptable; which you use will depend on how the sentence relates to its temporal context.
It's actually (1) which may be problematic:
(1) When she had entered the room, she found him laid on the floor with the box in his right hand.
This does have a combination of past perfect and simple past. It is formally acceptable; but it is difficult to conceive circumstances which would call for the past perfect in the when clause. Ordinarily the past perfect is employed to mark the action as unambiguously prior to the established past context (to the 'Reference Time'). In this case, however, where the RT appears to be found him . . ., there is no ambiguity; other things being equal, a when clause with a simple past non-stative verb is assumed to be prior to a simple past non-stative verb in the main clause. Consequently, the past perfect is unnecessary, and under FumbleFingers' Perfect Truism it should be avoided.
