Wayne,
The key to troubleshooting Com issues with the IntelliTouch is to understand there is just one com port.. You might be able to connect to the com port at different places, but there is only one com port.
The next key is that almost any device connected to the com port can load it down and cause the whole thing not to work.
Step one on troubleshooting the problem is to remove EVERYTHING from the RS-485 com port EXCEPT the main card and one IntelliFlo pump.
If you can get a single pump to work with the main card, then that tells you that the basic com port is working and that most likely that one of the disconnected device is bad. You can then add one device at a time until you find the bad one. The pump must show "Display not active" before it can be controlled by the automation.
Do NOT removed or connect any RS-485 device with the power on.. Unless your goal is to blow up the com chips...
Most things can be disconnected by simply removing the 4 pin connector.
Because of the damage to your surge card (SWCG power supply) I would suspect that to be the cause of your com port failure.. It may not be bad at all, but it could also have taken out other things on the com port including the chips in the cell itself.
Thanks,
Jim R.