That is quite some building, very interesting. Good photos. Filter drain outside looks a major undertaking and may not be possible if the rear wall is stone cladding to a rock face.
I see there are no gutters on the rear roof, normally I would suggest fitting gutters but there appears to be a whole hillside sloping towards this building so perhaps gutters would have minimal effect.
I think it depends how much money/time you want to spend. One way is as I suggested before, timber floor with air gap underneath and around the edges. Here is link to previous comment
Here is a link to the trada tables which give joist spans for different timber sizes, joist spacing, loading and timber grade
Free UK Span Tables for Floor Joists, Ceiling Joists, Flat Roof Joists, Rafters, Purlins - Timber Beam Calculator personally I would go for smaller timber size and more supports. For shelving you could buy some stand alone shelving. If there is a howling gale through there it may need a stud wall faced with something moisture resistant, not ordinary plasterboard,
You mentioned heated workshop with wood burner. In that case it is insulated floor with insulated stud walls set away from the stone walls so air can circulate under the floor and up the gap between stone walls and stud walls and out the top. Then we get to the ceiling, you could take the studding up to the rafters then fit pir insulation to the underside of the rafters, ensuring that air can circulate between the rafters. Problem is the translucent sheet roof lights. No point in spending a lot of money on pir insulation and let loads of heat out of those. You could board over them with pir insulation or put some form of secondary glazing, maybe get some double glazed panels made and fit them in a simple frame. Or get some double glazed panels out of some second hand windows. You could always do a heating calculation and see what the heat loss would be without doing anything to the roof lights.