Oh! Yes this was a big oversight of mine when answering your question. You are right: you have to explicitly include Jordan-Wigner string when using operators such as C^\dagger at the level of individual tensors in ITensor currently. (Other systems, like OpSum/AutoMPO include the string for you. This creates a somewhat confusing situation, but we are in the process of installing a much more 'automatic' fermion system - stay tuned.)
So then your code for measuring C^\dagger, if you are following Matt's recipe, should include extra lines like this:
s = siteinds(phi)
for j=1:i-1
Fj = op("F",s,j)
phi = apply(Fj,phi)
end
cdag_i = op("Cdag", s, i)
cphi = apply(cdag_i, phi)
inner(psi, cphi)