Dial #9 + 001,002,003 from an ICM dial tone (#9 = direct trunk select code). If you get no dial tone, the card supporting the 3 CO card may be bad. Since you already replaced the 3 CO card then a reset was done. Last resort is to try a factory default of the system.
Power off, wait for all LEDs to go out. Press and hold load button, power up, wait ~10 seconds then release the load button. A factory default should give you working phones and trunks.
FYI, v 1.03 is VERY old. You should upgrade to v 2.00. v 1.03 had some trunk issues. You may need to use WEBPro to upgrade since there was a bug with the PCPro upgrade. Upgrade your PCPro also. Both are free downloads in various web sites.