How to replace piston on cylinder six?

That isn't a good thing. A good machine shop would be able to machine it a bit, then weld up the low areas and then machine it back flat. Or it might be possible to deck the block and get it flat but that would take measuring the pistons to see how close they are to hitting the cylinder head. If they are too close material removal could cause problems.
The other option would be a different block.

Good luck with it, there are a lot of shops out there that can do the repair. Just need to find one that isn't booked for the next 2 years.

I would just clean them up. That could be oil or coolant hard to tell which. But if you go through the heads and refresh them it shouldn't be an issue when you put the engine back together.