OK, so the effin muons are too fast to be useful in the ground frame. How inconvenient?
So, obviously, that means we have to accelerate the h, d, t etc. fuel particles to the same frame as the muons. (Or, alternatively, electrostatically decelerate the muons to the ground frame).
For example, drill a 3 km-deep bore hole straight down (or, lease an abandoned oil well), and use a particle accelerator to fire your fuel species straight down at a speed comparable to the downward-plunging muons'. Some of them will end up running along right next to those ol muons, and they'll make friends as they jog along side by side, and maybe even hook up. (Vibrate your fuel beam through a teeny, tiny, microscopic angle just to give a little transverse nudge to that process)
Alternatively, build a big negatively charged grid, rather like a solar panel, to slow down the incoming muons, and have your fuel chamber right underneath your "muon panel".
Do you get net power out of any of this? Probably not. But hey, you wanted ideas for building a prototype fusion reactor using cosmic-ray muons, so there it is. (Note to self, patent these concepts)