I t seems like you plan to keep your fir floor. If you would like to fill gaps between flooring you will need to keep the flooring from moving too much so the filler will not crack and come out. If you take the opportunity to add some blocking from below before you cover the ceiling with insulation and wall board you can stiffen the fir floor so that the filler will not crack out. Half inch plywood strips, 2 inches wide glued with sub-floor adhesive in a quarter inch bead and fastened up with short sheet rock screws until the adhesive has dried will stiffen up the flooring enough. You could use colored putty forced into the cracks and gaps, too. Once the floor is reinforced you should not have leaks that could happen in the future.Kraft faced insulation should have the paper side up when it is installed, also, but this will only keep the fiberglass from getting wet, the sheet rock could get wet if enough water was able to leak through or around any gaps.
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