If you're using homemade bread crumbs (and it's definitely cheaper to than using store-bought!) you'll need to turn your bread into crumbs using a food processor.
In a medium sized pot, melt 2 tbsp of butter and add the breadcrumbs and 1/4 tsp salt. Sautee the crumbs until they're nice and dark and toasty. Pour onto a plate. Wipe out the pot to reuse for the sauce.
Meanwhile, bring a large pot of water to a boil (around 16 cups) and add 1 tbsp salt, stirring well to dissolve. This water should taste like salt water from the ocean. Add your pasta and cook until al dente (firm but not crunchy), according to package instructions. Drain well but do not rinse.
While wearing gloves (or a plastic baggie on your hand!) seed jalapenos and cut out ribs. I recommend trying a tiny piece of the jalapeno to see how spicy your specific peppers are - it can vary quite widely. Mine were grown in our garden and I found them quite hot, so I left out the seeds and ribs and only used two. You can adjust according to your own taste.
In your medium sized pot (from the breadcrumb step), melt remaining 1/4 cup of butter. Add 1/4 cup flour and whisk over medium-low heat for around a minute. Start to slowly add milk, a few tablespoons at a time. At first the milk will bind up the butter-flour mixture. Whisk until all the milk is incorporated, then add a few more tablespoons. Continue until you have a liquid mixture. Then you can add the rest of the milk called for.
Add spices, yogurt, cheddar cheese, Parmesan cheese, jalapeno, pepper and 1 tablespoon of salt to the pot with the roux and milk. Add drained pasta and mix well.
Pour pasta and cheese mixture into a medium sized (2.5-3qt) oven-proof dish. Sprinkle generously with toasted breadcrumbs. Bake in 350 degree F oven for 15-20 minutes, until heated through.