Welcome to the world of rescue and restoration (the wing and most of the rest of the work was too easy up until now)! About this point you start to wonder WHY you volunteered for this gig, but it all pays off in the end. Your Piper tail gives me flashbacks to the Cessna 152 I did, although yours still doesn't appear that bad.
My assumption for that sheet under the horizontal stab is that it not only sets the incidence but also gives a solid vertical surface to attach covering to. I agree that cutting the surfaces loose of the fuselage is the best bet, as once the covering is removed you're going to find stuff to fix which will be far easier on a flat building board.
The heavy cowl may work to your advantage - the plane was designed for IC and electric will probably weigh less, even with the batteries. I wouldn't worry about it at this point, even if some nose or tail weight is needed for proper CoG it'll be minimal on a plane this size.
Your A-Pillar has about a bazillion holes in it, probably from attaching the rear edge of the windshield. I'm guessing you already have thought about this, but now is the perfect time to patch those up and to make sure the A and B pillars are structurally sound and attached well to the fuselage and wing. Some CF layered in wouldn't be a bad idea based on the age and general quality of the build.