Timing Codes After Clutch Install

[iDriftYou]

So I recently posted a thread regarding a spun crank hub, codes I was getting were 130E20 and 130F20. I thought it was a SCH, when the shop pulled my old crank hub, everything in time correctly. After completing the CH job I still have these codes. We swapped out camshaft sprockets and still the same codes are present. Now I let them know that the clutch was changed and has around 50 miles on before these codes came up. The shop stated it could be the flywheel alignment. My question is that would a misaligned flywheel allow the car to run perfectly fine for the first initial 50 miles and then throw codes? I'm kind of stumped on what it could be, everything else has checked out completely fine. The shop did say that the timing pin that slides into the flywheel slots in but the motor is not at TDC when it slots in. The clutch is a spec super twin with a single mass flywheel. Any advice would be greatly appreciated.