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I have cleaned all the piston tops,and this is my first project of such a big magnitude,lol.I pulled one lifter out,wiped it down.looked brand new,so didn’t bother to look at anymore,I do know the car in 2009,was pulled and a stock cam,lifters,and chain were replaced along with a new radiator,water pump,seals and hoses,but the engine only has about 5,000 -6,0000 miles since.and it has 82,000 now.but,anything else I need to do before setting the heads,someone said I need the tread the holes out.
I would look at all the lifters. I took my engine apart to clean it at around 75,000 mile. I had 1 lifter that was pitted on the bottom, then I saw the 1 lobe was slightly worn. I ended up buying a new crate engine with a roller cam.
You definitely need to clean all the head and intake manifold bolt threads. You can purchase thread cleaner tools from Summit and others. You can use a tap but a thread cleaner is definitely a better way to go. You need good clean threads so the sealer your about to use on your head and intake manifold bolts have a chance to seal.
And I'm totally unclear as to why you felt the need to clean the top of your pistons.