You have to use ContracMetric:
expr /. ARules // ContractMetric // Simplification
A few additional comments:
1. Be careful, you are writing ^{-1} which creates a list. Compare:
2^(-2)
2^{-2}
2^{-2,-1}
2. Instead of the substitutions rules you have used, it is safer to use MakeRule:
FRules = MakeRule[{F0[i], gr[i] - ADOT[i]}]
ARules = MakeRule[{ADOT[i], gr[i] + Shift[-s] F[s, i] + Lapse[] \!\(TraditionalForm\`\[CapitalPi]\)[i] Gam[]^(-1)}]
3. Instead of 0.25, you can write 1/4 to avoid the 1. that you see in your result.