Yes, it will work, but do make sure you check piston/valve clearance anyway. Never hurts to be safe. I've done 3 E6 to E7 swaps without any problems. One thing that can help is a thicker head gasket. Make sure that the heads aren't milled too much either. That could cause problems, and don't use 1.7 rocker arms either. But I must ask you, why don't you fly cut the pistons when you have the heads off? There are tools that you can get that'll do it while the engine is in the car.
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