No, all pins are connected,

That's likely to be the problem. Click here.

should I rip out the other pins from my serial cable?

You could do that, yes. But if you want your docking connector to remain "pristine" for a resale in the future, then you should make a custom cable and/or connector that uses only pins 2, 3, and 5. This will also allow you to experiment with the TX and RX lines so you can get the connection right without an extra null-modem adapter.