The thing about cutting springs is that you can't un-cut a spring. So, if you're not sure how much to cut, cut less! You can always cut again.
You can do the math (you need the wire diameter, the coil diameter and the number of coils, you can Google either the formula or a calculator to do it for you) and determine what your resulting spring rate will be (approximately). Where things get muddy is in determining how much ride height you lose when you cut the spring. Since the free length of the spring is shorter, but the spring rate is higher... it would be complicated to calculate. Easier to just take a conservative guess and cut. With as much ride height as you have, I'm sure you can safely cut an inch, which is why I suggested it.
Will the springs fall out under full droop? Probably won't be an issue in the front. If you have a typical beam axle rear, a short spring CAN fall out. You'll have to be careful with that. If you end up with a really short spring, you'll have to put some sort of a droop limiter to keep the spring from unseating. You'll end up getting more wheel lift under cornering, but if a droop limiter lifts the wheel, the wheel obviously wasn't loaded, anyway.
Weight... yeah, I'm not sure what they'll allow you to cut out of a wagon these days. Used to be you could cut the whole roof if you wanted to. Maybe you still can if you leave the lower half intact for crash protection? Better ask before you cut.
For CG, you can see if it's possible to easily change the angle of the steering column for a lower driving position. Then get your driver weight as low and as far back as possible.
But, again, don't overthink it. Your finish position is going to have more to do with RELIABILITY than anything else. You should be under the hood making a list of all the things you need to replace and spares you need to carry. Belts, hoses, distributor cap & rotor, brake and clutch master cylinders, and so on. Trust me, you'll lose a LOT more laps even making a simple 30-minute repair than you'll ever gain by worrying about lightening the car or improving the CG!
I'd put the battery in the passenger footwell. Less battery cable = less weight. The battery requirements for such a tiny engine are very small, so there's not much weight there, not much need to worry about where it is... just don't add more to it than safety requirements dictate.
Lemons South 2008 - Fail, Lemons South Spring 2009 - Fail, Lemons Detroit(ish) 2008 - Fail, Lemons South Fall 2009 - Fail, Lamest Day 2009 - Fail, Miami 2010 (Chump) - 2nd!, Sebring 2010 (Chump) - Fail, Cuba 2010 - Crew Chief, Roebling 2011 (Chump) - 8th!, Sebring 2011(Chump) - 19th!