No, no, I wasn't talking about the wires inside the actual outdoor unit, just the two low voltage wires that come from the outdoor unit and further, I just wanted to make sure those two wires stayed where they were at in the furnace! It sounds like you did the connections correctly. Just to confirm:
On the furnace control board, on terminal Y, you should have one wire that goes to the outdoor unit (was always there), one wire that goes to thermostat Y and one little jumper wire that goes from Y to G on the furnace board.
Then also on the furnace control board, on the C terminal, you should have two wires, one that was formerly on G but now is connected to C at the thermostat and one wire that goes out to the outdoor unit that should have been connected there all along.
Also at the furnace control board you should have a connection from W at the thermostat to W on the board.
At the thermostat, you have both R terminals jumped together then to the wire that goes to R on the furnace board, then also a connection at Y, W and C that go to the same respective terminals in the furnace.
That is the full low voltage wiring for your system. If it's wired as above, your new thermostat should work with the exception noted previously that the fan switch won't do anything.