I have the GT-40 and I am using the stock valve covers with 1.6 roller rockers and I had to remove the baffle and do a bunch of grinding to make them work. I'm not sure if it makes any difference using the X heads as I am still using the stockers, but I don't see why that would make a difference unless the surface the covers sit on is higher than it is on the ET7E heads.
Save yourself the trouble and order a set of Ford Racing covers and a 1" phenolic spacer. It will look a lot nicer and involve a lot less work. Or wait until you get the engine and test fit your stockers to see if they will work.
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Too much to list. Best ET on the car so far with stock 2.73 gears - 13.73@102mph
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