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G'day Bastian. Sorry for not replying to this earlier. I missed the thread unfortunately!
It all depends on where you've got your ECU grounded to, and how the grounding scheme of the car is laid out. To have a battery in the trunk, you need to have a really good connection to the vehicle chassis where the battery is. You also need to have a good ground strap from the engine block to the vehicle chassis that makes excellent connection and cannot vibrate loose.
One thing I've noticed on the FD's, is that mazda attach their ground cables to brackets, which are then bolted to the chassis. There was a service bulletin from mazda that addressed this. If the vehicle had a stumbling problem at around 3000rpm, the fix was to clean and retorque the grounding points. I've just moved them to the chassis and engine block on my car. Page 75 of this document: http://www.wright-here.net/files/manuals/1993_RX7_Service_Bulletins.pdf