Okay, aluminum 6.2 block. i am putting in johnson 2110r lifters, headers, and f-35 TSP cam with pac .660 springs

i took the heads off to take a look at the cylinder walls and pistons. (see photo to see how they look). i am about to ask many questions to please bear with me.

How do the cylinder walls look ? should i be worried ?

unfortunately it looks like a valve knicked the top of the piston. Can i still use this piston ? why does this happen ? I have heard this can happen due to VVT but can anybody confirm ? engine has vvt and afm.

After spraying top of piston with brake cleaner and wiping with blue shop towels, carbon is still stuck on there. Is it important to get it off ?
Also the top of the pistons seem to have small lint on them(assuming from the towels), do i use a tac cloth to get that out ?

How do i clean the block head gasket surface ? i’ve seen so many conflicting statements about using red scotchbrite or green roloc bristle disc or a razor blade.

Lastly, the rest of my engine parts will come in within a few weeks. with one side of the heads being off, how do i properly store it to where rust will not form and contaminants won’t go into the engine. same with storing the heads ?

 

Looks like BAD scuffing on the cylinder wall. I would NOT assemble in that condition.
I'd get a ball hone in there, hopefully clean that up and install new rings.
Maybe fresh OIL pump too ?
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edit: I am NOT an experienced builder, so you may defer to the pro(s), but I have torn down engines at 144,000 miles that still had FACTORY cross-hatch, zero scuffing, and NO perceptible cylinder ridge. You photos do NOT show an engine that I consider " Ready to Assemble "

 

i believe what you’re looking at is just carbon building up from the pistons falling off. I would add better photos but i am not home unfortunately. and yes i have a mellings 10296 oil pump

 

Cylinders have no cross hatch left - they are too smooth - vertical scratches are not good.
Aluminum ls blocks are notorious for excessively uneven decks - not good for head gasket sealing.
The valve that hit the piston is probably bent.
Should be disassembled to check bearings and rods.

There is no sense trying to clean the head gasket surface - as you should have the blocks decked.
The bores probably have too much taper in them - so next size up pistons are probably in order - so no sense in trying to clean them.

Simple answers to your first 2 questions are 'Yes' and 'Bad'.

 

Yeah, that engine needs a rebuild for sure. Those cylinders are, at minimum, too glazed over to run as is. Tear it down, measure the bores with a dial bore gauge, and go from there. You may be able to reuse pistons if the bores aren't worn, but I doubt they're unworn looking like that. Also, in your 4th pic down, kind of hard to tell if it's carbon coming off or not, but it almost looks like you have a cracked ring land. If you want to really clean the tops of your pistons, bring them each to TDC and spray some Zep oven cleaner on them. Let it sit for a bit and scrub a bit with a plastic bristled brush. They'll look like new.