Been busy at work....and buying x-mas presents! A personal project is also taking up time for the next few months.
Back to business...
The seats which were replaced not being cut deep enough seems plausible. Especially combined with decking the head and block. A thicker aftermarket gasket can help here. That helps put the cam timing back to the design location and improves the valve to piston clearance.
However, don't cut the seats too deep. You reduce the spring load and increase the risk of valve float.
My only quandry is that SVT98.5 that there was 0.050in variance on exhaust and 0.030in on intake. Ok variance is a good number to look at, but what were the measurments? Which are the deep ones and which are shallow? Seat depth measurements are normally taken with very specialized gages (it's held to about �± 0.006in at the plant). I'm guessing that the shop measured off the bowl of a valve. That can work ok for comparison purposes. But you need to measure before and after. That way you can try to put the depth back to the design height.
