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Working with software handshake I believe you can jumper 6, 8, and 20 together and separately 4 and 5 together at the 25 pin Fadal connector.
And generally in this mode you would only need wires to 2, 3, and 5 at the 9 pin computer connector. I believe the other pins can be ignored. Your shield if you have one goes to pin 1 at Fadal.
As a start the setup at both ends should be 9600 baud, 7 data bits, even parity, 1 stop bit, and XON/XOFF (which is software handshake).
How long is your cable?
How is the Fadal grounded?
How is the computer grounded?
Try playing with a very short program. Post here a copy of a short test program. Maybe half a dozen lines.
If Edster sees this he maybe able to help you more and correct any misinformation I have given.
I believe you must start and end the program with a % delimiter.
Electrical noise could be your problem, but I would look for other issues first.