Usually I never seen over 12.8 on stock canned 93oct tune and that was at 5-6k rpm range but at mid range i'v seen 11.9-12.3. I never replaced fuel filter or FPR and my car has around 80,000 miles. And i believe previous owner never replaced it before too.
That would be the problem (suspect). I would replace that and see if it gets any better, we have them on the shelf, standard is shipping 3 day air.