I appreciate your post! Have any pictures?
I've replaced my driver and passenger mirrors with cameras, which is something you might consider. Parts are mostly from eBay and very inexpensive.
My guess is that you'll find you lose economy overall with the IMA battery removed; I've found weight reduction has very little improvement when compared with aero changes and reduced rolling resistance. Auto-stop can be modified to work at higher speeds (shut off engine when rolling downhill), and it's a huge fuel saver in the city. Additionally, any time the extra acceleration helps keep revs down, it's a net win.
You're also likely to lose a lot of fuel economy if you replace the curved hatch glass with a flat sheet - the slop of flat glass will be too steep and cause flow separation, which would defeat the purpose of extending the car with a boat tail. If you replace the glass, use something with a compound curve.
Have you yet removed your antenna base and rear winder washer fluid nozzle?
Would you be willing to post some pictures of your underbody modifications?