this is definitely an interesting application - and thanks for attaching these nice models. I think the doc link below can provide some helpful information for your measurements in Simscape:
I would suggest sticking to the force measurement in series. Simscape works with through and accross variables and the product of these two equals power in that domain (P = V*I in electrical, P = F*V in mechanical translation, or P = T*w in mechanical rotation). The through variables are always measured in series, and the across variable measured in parallel. In your models, if you want to place a gauge in parallel with the elements, then you should be using an ideal motion sensor (for x and v).
The controls part of the system (zpk and tf) heavily depends on the measurements being correct, so I would start by making sure that the response measurements yield good numbers and then re-visit the controls part after that. I hope this help and good luck!