I'm not sure if I completely understand your question... but here's what I think you are asking
There are 3 types of discrete ports (S-parameter, Voltage, and Current). Since you were able to specify a voltage I'm assuming that you have specified a constant voltage port which will deliver a voltage you define (1000 Volts) with a source impedance of zero ohms at all frequencies.
If an excitation waveform is user specified, you have to keep in mind that the value of 1 is the full voltage specified in the discrete port definition. In your particular case, when the waveform reaches a value of 1 the output of the port 1000 Volts, when the waveform reaches a value of 2 the output of the port is 2000 volts and so on.
It is often recommended to avoid confusion when defining a waveform is to make the peak amplitude a value of 1 and set the desired peak amplitude in the port definition.
The frequency domain signal should be a FFT of time domain results -- if it isn't, then maybe your frequency range parameter of the model isn't wide enough? That's the only thing that I can think of.... good luck