UPDATE: Not sure if it's going up to PCB design but apparently this one[1] seems to be the most praised on Amazon UK.
[1] http://www.amazon.co.uk/gp/product/0071771336?psc=1&redirect...
Or else you have the Bible of the trade, or "The Art of Electronics" by Paul Horowitz and Winfield Hill that just came out for a third edition. It's an incredibly comprehensive guide but you'd better have some free time ahead if you want to read through it all :)
2. Kicad is a very good PCB software package.
Word of warning though, kicad is currently in a state of "flux" with the latest stable from 2013, and the bleeding edge versions having all of the features you want to use. I personally use nightly builds and the 2013 version quite often, and neither are what I would call professionally stable.
Indeed, calling a prototype "final" before looking at the manufacturing side of things might not be wise.
* If you run a 9V battery into a linear regulator to get 5V, there goes 55% of your energy and battery life. Consider 4 AAA cells. Work on reducing standby power consumption. When idle, put the CPU to sleep until IR is sensed. (An ATmega can do this.) Things which burn battery power when idle fail as consumer products.
* "I could (and probably should) use an ATtiny for such an application but I only had some ATMega328 in my parts bin."
* Prototype plastic things with 3D printing. Manufacture them by injection moulding. The little injection moulder at a TechShop could bang out about one box a minute. Any commercial shop can turn out thousands in a day. Making the mould is either work or expense, but you come out way ahead after a few hundred parts.
Where are you getting your mould? Everywhere I deal with wants $5K+ USD NRE.
You can 3D print a lot of stuff for $5K USD.
(shameless plug, my username @ gmail.com if you would like to discuss what services I can offer you)