I don't think paddles are ever going to work, atari paddles (potentiometers) are specified for 5 volts. The portable is using 3.8 volts. Assuming the atgames chip is wired for paddles (no reason to believe it is) then the readout of the analog pots would be skewed. The portable is totally digital, paddles are analog. I don't think paddles will ever work on the portable.
Asaki, I found the six connections for the joystick (up, down, left, right, fire, ground). The other (+5v, paddle1, paddle2) don't exist on the portable circuit board.
I'm happy to post detailed pictures of how I did the mod..