I'm having great fun at the moment pruning very very overgrown and neglected soft fruit bushes. Well, in fact I've done them and just started on the blackberries - not so much fun
Here I don't prune top fruit until about March or even early April, and definitely not while it's frozen.
Your flaky bark could well be canker, which is a horrible disease which spreads to every tree. You would also see what look like soft rotten patches. You need to cut back to before any bits like that and disinfect your loppers/secateurs between
every cut. That sounds a drag but otherwise every cut you make will be spreading the canker into good wood. I use spirit or meths in a jar, with an old toothbrush to scrub the tools. It really is worth doing that - I have kept many of my trees going that way. If the canker is in the trunk the tree is lost.
Once you have cut back all rotten wood, stand back and see what your tree looks like. Hopefully you will have enough branches left to form some sort of shape. You don't need to prune the branches right back to a foot long - leave a bit more length, maybe 2 feet, and cut just below a bud which is facing either up or down but not sideways - this will give a better shape as the tree regrows. What you are aiming for is a goblet shape, with an empty centre for air circulation, and the branches evenly spaced around the trunk. The bud you cut above will become the new leader for that branch so choose it so it will grow on into a pleasing shape ie continuing the line of the original branch not setting out sideways. The new shoots will naturally grow upwards.
If these are apples, most apple trees bear fruit on spurs, which are short lengths of branch with about three buds on, growing out from the main branches - so prune any side branches back to those three buds.
So this will give you a tree with hopefully about 5 main branches, carefully cut back to about 2', plus a number of short stubby twigs coming off it where the side branches were.
All of this will cause the tree to put on a lot of fresh growth in spring, and all this fresh growth should be cut back in about June, to half the length of the new growth. Then next winter you can cut back the new growth again to the magic three buds.
A few apple trees are not spur bearers but tip bearers - you won't get any fruit at all on those this year as you will have to cut off all the tips.
If you have plum trees, don't prune at all until the summer. Pears should be ok and tend to look unmanaged anyway.
Don't be scared of pruning - if you get it wrong, the tree will grow out of it like a bad haircut. I dithered for years before I could take the plunge - the final straw was when my OH pruned all my espaliers into normal tree shapes and I realised I would be better to do it myself