My reloading system (Hornady LNL Auto Progressive) got a little dirty down by the part that presses upwards and seats the primer. I didn't realize it and this led to the part unscrewing a little. This meant it fell out of spec, and my primers seemed seated, but weren't deep enough. Had very similar problems to what you are describing.
Is your firing pin spring the reduced power version? If not I would order one just to get the most out of the 13 lb hammer spring. CZ Customer and Cajun Gun Works both have them. The extended firing pin, reduced power firing pin spring, and the 13 lb hammer spring should ignite everything 100% of the time. As was mentioned, the reduced power trigger return spring has no impact on the force of the hammer impacting the firing pin, so your upgrade to that part bears no weight in the issue.