> SG filter requires equally spaced X values. Apparently your data do not satisfy that criterion. One solution would be to interpolate your data (Analysis > Interpolate/Extrapolate) over a range of equally spaced X values and filter the results.
Origin has peak picking routines that will give you the positions of peaks that satisfy given criteria (height, width). Knowing their positions you can find their heights. See the Curve object and peaks() function in the LabTalk reference. You can also use Pick Peaks on the Tools menu. But I'm still not sure what you mean by peak to peak amplitude. Difference between adjacent peak heights?
Probably easiest with the Pick Peaks tool. Adjust it to find all peaks then locate and add a column to the output worksheet Peaks1. Select the new column, select Set Column Values, enter the expression diff(col(Pky)) in the dialog and click OK.