All Pairs Shortest Path Fewest Stops
This problem cannot be solved using a (modified) Floyd-Warshall Algorithm. The underlying assumption in F.-W. is that all paths arriving at a given node can be extended along the same path to the destination. Therefore choosing the shortest path that arrives at a node is also optimal for all paths that pass through the node. By adding the fuel constraint, this assumption is broken.

More generally, problems of this form are called the Resource-Constrained Shortest Path Problems and are, in general, $\mathcal{NP}$-hard. A generic solution to this problem is to enumerate all feasible paths that lead to any node in the graph, which obviously leads to exponential time complexity. In practice, "dominance" rules are applied to prune partial paths that are clearly inferior to other partial paths; in your case such a dominance rule could be to throw away all paths arriving at a node with more refills and less fuel than another path arriving on the same node.