you probably first want to enable @local_scaling on your phys.multiple object.
this will allow you to send the scale matrix values (as you're currently doing each frame), without causing a body reset.
then, you simply plug the pak you've created into the phys.multiple.
you set the body using position matrix cell index.
so in your example, you have a position matrix of dimension 100, so you would use 0 to 99.
if your position matrix was 10 10, it would be 0 0 to 9 9.
you can alternatively send to bodies using the body name. the body name is the phys.multiple name (set using the @name attribute) followed by an underscore and the cell index.
eg: pmult_0 to pmult_99, or if it's 2d, pmult_0_0 to pmult_9_9
the phys.picker will output this name when clicking on phys.multiple bodies, as demonstrated in the patch i posted above.