Pour 2/3 cup sugar over the base of a 12-inch braising pan or large baking dish.  Layer half the tomatoes, overlapping the slices, in the pan over the sugar.  Sprinkle with 1/3 cup sugar, and top with the lemon zest, lemon juice, cinnamon stick, fennel seeds, and chiles. Top with the remaining tomatoes, followed by the remaining cup of sugar. Let sit for 30 minutes. 

Preheat the oven to 400°F.

Place the pan, uncovered in the oven, for a total of about 2 hours.  Before long, the tomato juices should simmer actively.  After 1 hour, check to be sure the tomatoes don't appear to be dry on the top layer.  If so, baste with the juices that have formed. 

Continue to check every 20 minutes, spooning the juices over the top tomatoes as needed.  Remove the chiles if they char.

The tomato juices should begin to gel at 2 hours, but it could happen a little sooner or later.  Test the juices by spooning a little onto a plate, letting it cool, and running your finger through it.  If it holds the line, the jam is ready. Remove the jam from the oven and let it cool.  Remove the chiles and place the jam in jars to be stored in the fridge until ready to enjoy.