Great job on the mod. It looks like a well designed system.
I predict that your 'new' 2.5" loft top-bag will keep you toasty, even below 30°, provided you place some closed cell foam to the top of your Clearview. The Cuben bottom will reduce losses to moving air, but not convective losses to the ground.
Do you (or anyone) have any experience on the puncture resistance of the .33 ounce Cuben? Just how careful must one be to keep it waterproof?