Pistons generally won't come out of the bottom of the block even with the crank out. Though I did do this once with a V6 Buick that needed a single connecting rod replacement / crankshaft and by chance the bad one was the only one with block clearance.

I'd use medium / light scotch brite to gently clean the bores up to remove any high rust spots before removing pistons from the top. Use a vacuum then clean the grit out with brake cleaner. I would not reuse piston rings from any of the rusted bores and would only reuse the rings from unrusted bores if they were $$$$$$ and I was building a "good used" engine rather than a full on rebuild.

You can unbolt the bell housing from the engine and pull the trans off the engine then access TC bolts from there. Just drain the TC or be ready for some fluid loss. Given the engine was sitting for an extended period of time the TC may have drained out.

Another path of attack is to remove the oil pan and pull pistons from the top that you can access with the crank in it's original position then rotate to where pistons in rusted bores are moving downwards so you can clean the bores. This way at least you are minimizing the number of times pistons need to go up and down.