First thing's first: What do we do with Driver?
Driver is out and restricted to the dugout under rule 2-36-3 (a). The next batter is Woods.
2-36-3 (a) . . . An illegal substitute is:
a. a player who enters or re-enters the game without eligibility to do so, or..." Rationale: Clifford became legal once a pitch was thrown to Dillan, so Driver did not have eligibility to re-enter the game. Therefore, the only person illegal here is Driver.
Now that our illegal substitute matter is resolved, what do we do with Clifford, since he and Driver share the same place in the batting order?
I'd say we do nothing with him and his advance is legal. His stats are recorded in Jones' spot in the scorebook, and an out is recorded in the #5 slot in the batting order.