It seems odd that two plugs would be misfiring at the same time and they began doing it at approx the same time.
Have you checked the primay and secondary side of the coil? If I were guessing I would swap 4 plugs around into 2 & 6 and see if the problem persists at those same cylinders.
Do the pickups on the cap at 2&6 look similar to 1,3,4 & 5? Don't be surprised if your new cap is defective.
X2 on the HEI ($26 from my local U-Pull-It)
Good luck
