You only need one pull-up resistor (4k7) per I2C pin: one for A4 and one for A5.

using 2 linear regulators and power half the devices with other and the other half with the other.

This should work just fine.

also what is the chance one of these will break and surge 12 volts through my 100's of dollars in sensors and Arduinos?

They usually break because the load (current) is more than they can source (check the datasheet).
From what I reckon, a broken regulator would not provide any voltage (rather than allow the input voltage to go through).
You can get a 5V/3A switching mode regulator on ebay for $5 or less.

This may be useful:
http://timewitharduino.blogspot.ca/2012/04/bookclock-software-update-set-time-from.html
I built a clock with this display. You can easily extract just the displaying code.

Then you should also straighten/shorten some traces (in the upper right side, there is one awkward sticking out).
Pull-up resistor on the reset pin?
Power-indicator LED with no resistor?
A schematic would be also helpful.

I would add a ground plane, among a few other things.

If can replace the "flip dot" with an electromagnet that opens a gate and makes something (e.g. ball) fall through.
The electromagnet may take 10mA or so.
A simpler solution is to involve a battery powered quartz clock. You power the clock (so the seconds hand moves) for as little as possible at the end of the time-cycle, but as much as to make a visual difference.
Interesting challenge, I would like to see it working in practice.

Or buy the parrot drone
http://ardrone.parrot.com/parrot-ar-drone/select-site
and hack it.

Aren't these front panel supposed to be custom made, to your own specs?
Draw one, then get it laser cut.

You can also use a relay.

Did you see this project?
http://www.ladyada.net/make/tweetawatt/

I am guessing 2 are for the LED, and the other 3 are for the switch itself.

The funny thing is that even a "traditional" microphone-based transmitter, with a proper oscillator, is quite often challenging to build and troubleshoot by a beginner.
Honestly I don't expect this to work as a "voice/noise transmitter" in the real world.

This looks like a solid one:
http://www.seeedstudio.com/depot/metal-push-button-momentary-w-blue-led-p-660.html?cPath=156_160

create a server in my laptop which saves data of any RFid detected and can provide data to Arduino for further use

How is your laptop connected to your Arduino?

What firmware are you running on the ATTiny2313?  Everyone, myself included, can not get the bootloader to verfy after 64kB.  The 664p 644p is ok, but the 1284p is too big.

I get the verification error too, and I disregard it. The bootloader is burned just fine.