The first purpose of this paper is to solve completely the finite field cone restriction conjecture in four dimensions with $-1$ non-square. The second is to introduce a new approach to study incidence problems via restriction theory. More precisely, using the cone restriction estimates, we will prove sharp point-sphere incidence bounds associated with complex-valued functions for sphere sets of small size. Our incidence bounds with a specific function improve significantly, a result given by Cilleruelo, Iosevich, Lund, Roche-Newton, and Rudnev.