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The only thing I am aware of on the drivers side of the trunk is a white plastic vent piece. On the Nak. system the amp is on the passenger side of the trunk. On the Pioneer there is only one amp as previously described. Percy, one of the other memebers, has a really good book on the subject.
For ls400, the Pioneer Premium system: the head unit has a built-in amp which drives the 6 speakers (4 on front doors, 2 on back door), and the thing located in the trunck on the dirvers side next to the fuel tank is the amp for the trunk's subwoofer. (I have a 91 ls400, with Pioneer system). From what I understand that the Nak system has a separated amp that drives all 6 speakers and the sub. (not sure where the amp located, I don't think it built-in with the head unit).