Combine onion, habanero peppers, lime juice, and salt in a bowl; cover and refrigerate onion-habanero salsa while preparing and cooking the pork.
Place guajillo peppers in a bowl; pour enough hot water over the peppers to cover. Soak until peppers are softened, about 10 minutes. Drain.
Heat oil in a large skillet over medium-high heat. Season pork with salt and pepper on all sides; cook in the hot oil until completely browned, 15 to 20 minutes. Transfer the pork into a multi-functional pressure cooker (such as Instant Pot(R)).
Combine guajillo peppers, orange juice, vinegar, achiote paste, and garlic in a blender; blend until smooth. Pour the sauce over the pork cubes in the pressure cooker. Close and lock the lid. Select high pressure according to manufacturer's instructions; set timer for 45 minutes. Allow 10 to 15 minutes for pressure to build.
Release pressure using the natural-release method according to manufacturer's instructions, 10 to 40 minutes. Unlock and remove the lid.
Remove the pork to a serving dish and shred with 2 forks. Pour the achiote sauce over the shredded pork. Serve with the onion-habanero salsa.
