My electronics is way out of date, there may be a better way to do this now. I had a similar problem to this many years ago (1983) when I designed and built a medical instrument. I was measuring the heart muscle impulses (ECG) but then doing signal processing on them using electronics and computers. It was considered highly desirable not to electrocute the patients
so I had optical isolation between the two. This got me around any problems with varying volatge levels keping the patients safe.
My thought is that you need a box of tricks with something like an optoisolator or equivalent to isolate and invert the pulses feeding the inverted ground referenced +ve pulses into the hand controller connection of the Tak EM 200.
I'd also put in a mode switch (might have to be an 8P8T switch) and connector so you can plug the handbox into and switch into the scope side of your box to control it manually for pointing and centering objects.
Hope that makes sense. I can also ask an up to date expert I know for some advice if you need me to.
regards
Joe