I am the happy new owner of a SR5 4Runner (even though I let go of my 2005 4Runner and it broke my heart to see it driven away), but I have spent some time in the past 24 hours that I have had the new Runner fiddling with the Bluetooth stuff. First, if you have a non-nav head unit, and a Droid (first Moto Droid), good luck getting all your contacts into the car phonebook en mass. Believe me, I have tried EVERYTHING. I gave up and just manually uploaded a few contacts one at a time. My Droid is rooted, and is running a vanilla 2.2 Froyo ROM, so I am in your boat too. I think it has to do with the head unit, and not the phone.
I would turn off the bluetooth on your Droid, turn off the car, turn the car back on, turn on your Droid's bluetooth, and then try pairing again. If that fails, try rebooting your phone.
BTW, are you running a custom ROM or just running a rooted Droid? If you have a custom ROM, try a different ROM and see if that works.