There's a switch stack mounted on the bottom of the drop target bank that only closes when all the targets are down. You would have to add an additional switch to this stack, then rewire the common path for all of the dip target switches to go through your new switch.

Switch Stack

I don't have my Royal Flush any more but check the score cards for 3 and 5 ball it seems to me there was some sort of change on those targets with the changing of how many balls you have the game set too

I went and looked at the instruction cards for Card Whiz. You're right; 5-ball play has this additional instruction: COMPLETING DROP TARGETS LIGHTS CENTER TARGET FOR 3000 POINTS.

So it appears that the 3000-point dip target routes through the switch stack on the drop target bank on 5-ball play, but bypasses it on 3-ball play.

This makes it a little more complicated to accomplish what you want to do, but it's still doable.