Add all ingredients to a medium-sized pot and simmer over medium heat.: The first sensory cue is a gentle, rising steam and the popping of fruit skins, a soft simmer that smells intensely of fruit and citrus. Simmering allows the juices from the cherries to loosen and mix with the orange juice and maple syrup , producing a fragrant, ruby colored liquid. Stir occasionally to prevent sticking and watch the surface, skim off any foam for a clearer jam. A common mistake is simmering at too high a heat which causes rapid evaporation and burnt flavor, so keep the heat moderate and patient.
Cook for about 30 minutes or until cooked down and thick.: You will notice the mixture become syrupy, the bubbles slowing and the color deepening to a glossy jam. When a spoon dragged across the bottom leaves a trail, you have reached the right thickness. The aroma will intensify and sweet notes will deepen. Avoid rushing by increasing heat, which risks uneven cooking and bitterness. If the jam seems too loose after cooling, return to low heat and reduce further.
Jam can be made the day before.: Make ahead affects texture and flavor positively, the jam maturing overnight so it tastes more integrated and less one dimensional. Chilling also helps it set fully without additional reduction. A typical oversight is not cooling the jam before refrigerating, which can trap steam and cause condensation; allow it to cool to room temperature first for best results.
Preheat the oven to 350 degrees F and spray a 12-count muffin tin with non-stick spray.: As the oven warms you will smell faint warmth and readiness, and a comfortably even oven temperature ensures the custard sets uniformly. Coating the muffin tin prevents sticking and helps unmold the cups with clean edges. If your oven runs hot or cold, use an oven thermometer to maintain accuracy. Not preheating can lead to uneven baking and soggy centers.
In a large bowl add eggs, milk, yogurt, vanilla bean paste, almond extract, and kosher salt. Whisk to combine.: The mixture should look glossy and pale as air is incorporated, releasing a fragrant note from the vanilla bean paste . The whisking step distributes the eggs and seasonings evenly so the custard sets with a consistent texture. If you stop whisking too soon you may find streaks of egg white after baking, while overwhisking is not a concern here. Be careful to get a homogeneous mixture for smooth results.
Add in the bread and toss to coat. Let the mixture sit for about 5 minutes so the bread has time to soak in the milk.: You will hear a soft plop as the bread soaks and see it swell slightly while darkening with custard. That short resting period lets the center of each bread piece absorb liquid, creating a tender interior when baked. If you skip the rest the centers may remain dry, and if you soak too long with very soft bread you risk a mushy texture, so five minutes is a balanced window.
After resting stir in the almonds.: When you fold the sliced almonds in, they release a toasty scent and provide flecks of texture. Adding them after initial soak keeps some crunch intact after baking. Mixing them too early into a very wet mix can result in soft almonds, so this timing preserves contrast and adds a nutty breadth to every bite.
Add bread mixture into the prepared muffin tin and fill each one about half full.: As you spoon the mixture the cups should glisten and hold shape, the custard clinging to each piece of bread . Filling halfway allows room for jam and a top layer of custard soaked bread, ensuring even baking and avoiding overflow. Overfilling will cause spillover and underbaking at the centers, so keep the fill consistent across all cups for uniform results.
Place about 1 tablespoon of the cherry jam on top of each cup and then top with the remaining bread mixture.: The jam will sit like a jewel in the center, creating a concentrated burst of cherry flavor once baked. Topping with more mixture seals the jam inside and produces a marbled appearance on the surface. Avoid using too much jam which can make the center runny, and be mindful to distribute it evenly so each cup has the same balance.
Bake for about 35 minutes or until fully set.: During baking you will notice the edges turning golden and a faint nutty aroma from the sliced almonds . The custard is ready when it feels springy to the touch and a knife inserted in the center comes out mostly clean. Baking too briefly leaves a wobbly center, while baking too long can dry the cups, so monitor closely in the final minutes and trust the visual cues of golden edges and set centers.