Decking the head won't cause the pistons to hit the head, it can allow the pistons to contact the valves if the seats aren't cut to lower the valves to the correct depth.
Any time the block is decked piston protrusion must be checked to see if a oversized head gasket is needed.
With a decked block, milled head and higher lift cam you could have pistons and valve kissing each other.
My block had been decked .010, pistons protruded .008-.012 above spec requiring a .010 over head gasket. Valves where at min spec depth and I had installed a Colt stage 3 cam bringing valve to piston clearance closer than recommended.
To prevent possible issues I installed a .020 over head gasket, 12k miles of heavy towing with no mechanical issues so far.
For S&G's loosen the valve adjustments another .010 on every valve. You'll have a noisy valve train but if the other noise goes away you'll know what the problem is.
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Mine: 04 F-450 sc 4x4 fb drw 5.9 12v 215 ppump, zf6, kdp fixed, 3k gsk, AFC Live, super b single, pusher intake, d-celerator ebrake
Hers:2018 F-150 sc 4x4 5.0
Farm trucks: 01 Z71 ext cab, 95 S10, 93 F-800 8.3 Cummins, 87 AM General 5 ton
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