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The trick is to disconnect the aerial labelled BT from the bluetooth module and connect the spare WiFi aerial instead.

I had my 2006 Mac Pro replaced to try and fix this issue, though the replacement had the same problem, and an authorised repair centre couldn't fix it either. So I switched the aerial myself.

I've been happily using a Bluetooth mouse, keyboard and graphics tablet with mine for the last few years. The current aluminium Bluetooth keyboard and Magic mouse work fine.

Awesome fix. I was able to rewire the BT antenna on my '07 MacPro (3.0 dual/dual) and now the Magic Mouse works perfectly. Good thing too, I was about to repackage it for return.

This is the diagram I found through following the links on this thread:

BT: disconnected
1: to bluetooth module
2: upper airport connector
3: lower airport connector.

Getting the short #2 wire connected to the upper airport connector was a hassle. But eventually I was able to connect it. I switched the rubber boot that was covering the unused #2 connector and put it on the BT wire.

I'm stoked. :)
 
The only problem I have with my 2008 Mac Pro and the Mighty mouse is that, sometimes, the "secondary" button press doesn't work, and it counts as a normal press.

I don't know whether the fact I use the 5ghz band for Wi-Fi might make a difference, since bluetooth uses the 2.4ghz band. Possible.

I use an USB mouse, though. I wanted the full sized keyboard.
 
I just did the switch because my bluetooth would sometimes just get quirky when I was within 3 feet of the computer. I have a bluetooth mx revolution and it would get jumpy and not respond, as if the batteries were going out.

I changed the label, putting "2" onto the bluetooth from the mainboard.

So far so good.
 
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