The dough is meant to be sticky. Adding flour to fix it is what makes the finished pastry tough. If it is too slack to roll, chill it for 15 to 20 minutes and use only a light dusting on the worktop.
Drain and squeeze the sauerkraut properly, and cook the mushrooms until the pan is dry again. Wet filling is what makes the bases soggy.
Go easy on salt in the filling. The sauerkraut brings plenty, and many Polish cooks add none at all here.
Leave room on the tray. These swell in the oven, and pasties set close together will meet and tear when you separate them. Two trays or two batches.
Freezing: dough or baked, not in between. The dough freezes well before its first rise, and fully baked pasties freeze and reheat from frozen in a hot oven. Shaped but unbaked is the one stage to avoid.