You more than likely have incorrect torque converter bolts. Torque converter bolt heads are thin vs the hex heads of common bolts. Have you verified what type bolts they are? A thicker flexplate will simply position the converter a smidge further away from the crank (into the trans) at least from what I’ve seen. And the dust cover (there are quite a variety) is installed with any ribbing protruding towards the engine, not towards the trans right?