If they are both series 3 then I doubt there is a difference. There is some speculation that the 04 doesn't have powder metal rods, but hasn't been proven... If its series 3 vs 2 then I would go with the Series 3.
The series III has an aluminum oil pan and doesn't use the U shape 3800 bracket. That bracket can be modified to fit with some grinding. Its a non issue if you are making your own mounts. The aluminum oil pan has added benefits in that it wont leak and you wont lose oil pressure around tight turns.
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Turbo 3800 E85 5spd spec5
11.53@126.7