Allow the user to set measurement reference points on each signal separately. It's also not too difficult to copy the input annotation file, writing the measurements into the num fields of the annotations, so that WAVE can display them as a signal. The measurements as made above are very easily contaminated by small amounts of noise in the signals. You should be able to improve them significantly by averaging the amplitudes of several samples in the neighborhoods of the isoelectric point and the ST level measurement point. The program should not produce measurements for ventricular ectopic beats, or for beats that are extremely noisy.
Noise detection is an interesting research problem in itself.
Another source of measurement error is baseline wander in the ECG, visible as slopes in the intervals between beats. You can reduce this error by modelling the baseline drift and subtracting it from the signal. Simple linear models, or quadratic or cubic splines, can be used.