Pictures would be very helpful. =) There are plenty of things you can try.
- Use a larger dock connector. I don't know which one you're using, but if you use the one I always use, the one that snaps shut or Ridax model A or E, you'll have loads of room.

- If you used 28 AWG for all wires, I think you'd be okay. USB 2.0 specifies 28AWG for the data lines, and between 20AWG and 28AWG can be used for the power wires. If you use individual wires without the rubber sheathing, shielding and so on, I think you'll have more room to work with. To compromise for space sake, I think anything thicker than 24AWG for audio is pushing your luck.
- Use the same ground wire for audio and USB. They're all connected together on the logic board anyway, so exclude one wire from the dock. You eventually need to shield the USB wires, but I think it'd be okay if you omitted most of it within the dock connector; just make sure it's still connected to ground before it leaves the dock.
- Don't connect the USB shield. I know it goes against what I just said, but since it's already connected at the computer end, maybe it's not entirely necessary for you and it gives you extra room.
- Push the 22uF caps into the corners of the dock connector.
- Use 22uF instead of 47uF.
- Leave the hot glue and epoxy out unless
absolutely necessary.
Those are some things you can try. I can't guarantee it'll work, but if it all works out inside my head, surely it's going to work out fine.

Let us know how it goes.