There may be too many questions here. I'll try to hit some of the high points of the technologies, but be aware that you could write an entire dissertation on the matter (mine was on a closely related topic).
- The incoming electron or proton beam is characterized by using current monitors (inductive, resonant cavity, charge cups, etc) and by measuring its bending radius in known magnetic fields.
- Scattered electrons (after the collision) are detected by there ionization in interactions with matter, by Cerenkov radiation, and/or by transition radiation. Their momenta are again, characterized with magnetic fields.
- The detection of the reaction products use the same techniques as for the scattered electrons.
- Filtering the junk to get just the events you want is a big topic. You put a lot of effort into designing the detector package, trigger, data acquisition, storage subsystem, and analytical programs to make it happen. This is what keeps grad students and post docs employed.
Finally, baryon targets are easy: put any matter made of protons and neutrons (i.e. everything) in front of the beam, or collide electrons on protons. Meson targets are hard: you can't just get a pile of pions because they decay. Fast. So you have to generate a meson beam (which is a bit of a trick in and of itself) and direct it into either a fixed baryon target or another beam (electrons, say) in collider mode.
Now some physics. You don't follow a single electron through multiple independent scatters in a single collision with a hadron (the time and distance scales are prohibitively small).{*} Instead, you chose a center of mass energy for the collision that will tend to suppress the effects of scattering from the whole composite object, and allow you to look as the electron-on-valence-parton cross-section.
That measurement tells you (after various corrects are factored in) the sum of the squares of the parton charges, and you already know the sum of the parton charges.
{*} Actually my dissertation concerned itself with detecting the effects of secondary scattering events in one very closely defined circumstance and how the rate of such scattering might{+} depend on a parameters of the collision called $Q^2$ (the squared four-momentum transfer).
{+} The theorists had said we might see an interesting effect at 5--10 GeV$^2$. In the eight years it took to design the experiment (to get to about 8 GeV$^2$), get approval and beam time, and set it up they'd changed their minds. "It's outside your experimental by a factor of two or three" they said. It was a world class, high-precision null result.