it's nice to know that it's now working.

if you haven't used any other wiring with your UNO, it can be ensured pretty easily that you haven't screwed on your UNO(That's definite.).

Try Connecting both the Arduino's at same time ,then donot start your arduino IDE just look for the Windows prompt ,it should come afresh because the other one UNO(DIP) is connected and recognized as the specific driver is installed that catches up with the com3 port. then plug in the SMD now it should prompt for a new device connected then install it's .inf (and yes UNO's have no DRIVER's, they have .inf files which makes UNO better for newer WINDOW version's).

i always plug it out without any problem's till yet (UNO and 2009 not problem)

attachment to the VIN must not be a serious problem because the circuitry is not supplied anything from here only the direct unregulated current flows however in the 5V and 3.3V pin's are regulated for power as such the wrong temp.. sensor link doesn't seems to have made wrong doing's.

Well at least it uploads sketches faster.  

right atleast this is provided, However to an Experienced user the 8u2 will come handy to turn Arduino into anything like mouse , but the sad thing is that all the 8u2 pin's can't be used.

possibly you didn't kill it , however if you have ensured it's not making any short-circuits, and no 2 motor's can make your arduino go dead , if wrongly wired then the motor's will not just work that's it,
unplug the arduino>give a restart (Computer)>plug in the Arduino again.

in most of the cases this remedy work's as in mine(had seen such problem a lot many times had one even today)

what's the present status ,did you make it work?

Most probably something wrong happen when your ZIP file extracting approached avr compiler file's

I have tried the same many times. i own a UNO and 2009 but UNO is something different with the Bootloading thing because of the Optiboot Bootloader(to the minor extent), Initially the FTDi chip used to act as a mere SERIAL PORT but with this UNO ATmega8u2 act's a lot differently which provides you with other abilities, so it's not done with me regarding the Bootloading using UNO for such reason's

I'm not clear upon what your plan is?,However you can configure other digital pin's as Input also if you're falling short of inputting pin's.

Analog pins are HIGH impedance pins which mean's if they are configured to give power to external circuitry they are less capable than the LOW impedance digital pins 0-13(they can provide 5v @ 40mA to any circuitry competently ) ,could be this thing or else 20K pullup resistor's are there at each digital and analog pin

Other ATmega/AVR
To use a different ATmega/AVR chip, you'll need to make changes to the Arduino core, which is in the hardware/cores/arduino sub-folder of the Arduino application directory. This shouldn't be too hard, but it will require reading the datasheet for your chip. In particular, the names of registers and register bits are likely to vary between microcontrollers.

Which Files i need to Modify in the hardware/core/arduino to accommodate different ATMEL AVR's and what would be the modification?

Thanks Coding badly!

I know that's why i defined the ATmel too, i wanted to know the Atmel AVR's compatible with the Arduino or Capable of being programmed by Arduino.