The name of the level is a hint. What do you need to swap?
How about a reactor which inputs a nitrogen atom and methane and performs some clever bonding, and then output ammonia and a methane radical (CH).
If you split up the nitrogen in to two pipelines of nitrogen atoms, one can go to the swap reactor and the other can go to the cyanide constructor. Plenty of drive-thru unbonding or bonding opportunities here.
Swapping is quite simple, it requires a little bit of syncing. A good place for the bonding plates is over the methane input.
To swap, one waldo inputs a methane, unbonds it and pulls a CH to the output. It also starts the other waldo which takes a nitrogen and bonds it in to the hydrogen atoms which are still on the bonders. Make sure the molecules don't crash.
Here is a swapper.