Laura, you said that after tying the two blacks and red together in a J box the kitchen are no longer switched ,,,did you mean that the kitchen lights stay on constantly now and the kitchen light switch has no effect on those lights??? therefore I assume you wired the three way switch (under the house!!) back into the circuit to recover kitchen light control! is the switch in the kitchen a three way switch too???
And also ,,,,this three way switch was paired up with another three way switch in the den??? and you have two other three way switches wired up working in the den too???
sorry for all the questions, trying to visualize your wiring diagram sounds like a mess.