As a first step, I would lift the playfield and start a game (don't forget to keep the return hole switch closed until the kicker tries to kick the ball into the shooter lane, and then briefly close the trough switch with your finger so the game thinks a ball is ready to go).
On the underside of the pf, on the left side and down toward the back of the machine, there is a bank of latching relays. I don't remember how many there are, but the first 3 going from left to right are labeled 1B, 2B and 3B. Those are the latching relays for the jokers - green, white and purple. Using your finger on the pf to close switches, watch to see if those relays are firing and latching. For example, when you hit the green joker target or rollover, the 1B relay should fire and you should see it latch. White joker target or rollover should fire the 2B relay, and purple should fire the 3B relay.
If they are firing and latching, carefully examine the switches on those 3 relays and make sure they're clean and opening/closing as they should in the latched and unlatched positions. That whole bank will tilt down for easier switch access if you loosen the 2 wingnuts on the sides. (Make sure those wingnuts are tightened to begin with.) There are a whole mess of switch tabs and wires at the other end of those switches - look closely there too for shorts/broken wires/bad solder connections.
If they're not firing, we'll have to figure out why that is. I'm guessing that since the 4000 pt scoring works, that they are firing, and it's more of a switch problem, but I'd start with that.
By the way, this snippet isn't supposed to show you how the 1K-4K scoring works, just to show how the latching relays are fired.
Royal Flush latching relays (resized).JPG