I don't think that all components of the Windows version of the IDE are 64 bit compatible.
The only way that I could get the IDE to work with an external version of Java on Win 64 is to install the 32 bit version of Java.

[Drivers]

It's not clear from your post if you have followed these steps to install the com port drivers:

Right click the "Arduino Due Programming Port" in Device Manager
Select Update Driver Software
Select Browse my computer for software
Click Browse button
Select the Drivers folder under the location of your Arduino software installation. (Do not select the FTDI folder inside the Drivers folder)
Click OK
Click Next

See this commit:
https://github.com/arduino/Arduino/commit/85bf4252f0bfaf7fb86111c2104eb089c3a67496

They updated avr_tools.zip with the 5.11 version of avrdude.

Avrdude 5.11:
http://savannah.nongnu.org/projects/avrdude

Have you loaded the Prolific drivers:
http://www.prolific.com.tw/US/ShowProduct.aspx?p_id=225&pcid=41

Pay special attention on that page about Win8 not being supported by certain versions of their chip

NOTE:

Windows 8 is NOT supported in PL-2303HXA and PL-2303X EOL chip versions.
Run PL2303 CheckChipVersion tool program in Windows XP/Vista/7 to check chip version.
Prolific recommends to buy PL-2303HXD (HX Rev D) chip.

You will need to apply this commit to your Arduino code base to solve your problem ( a release with this fix has not been made, yet ):
https://github.com/arduino/Arduino/commit/70351fc34150b1288079996839082e751b176821

Read this thread for all the details:
http://arduino.cc/forum/index.php/topic,129869.0.html

With the changes above, you should uninstall the driver, change back the .inf to original, then install the driver with the original .inf

Actually, avrdude 5.11 was released with Arduino 1.0

Follow the steps here to disable driver signature enforcement on Win8:
http://arduino.cc/forum/index.php/topic,94651.msg727588.html#msg727588

Then follow these steps to install the UNO drivers:

Right click the Unknown Device in Device Manager
Select Update Driver Software
Select Browse my computer for software
Click Browse button
Select the Drivers folder under the location of your Arduino software installation. (Do not select the FTDI folder inside the Drivers folder)
Click OK
Click Next

[Drivers]

Here is the procedure to install the Arduino drivers on Windows:

Right click the Unknown Device in Device Manager
Select Update Driver Software
Select Browse my computer for software
Click Browse button
Select the Drivers folder under the location of your Arduino software installation. (Do not select the FTDI folder inside the Drivers folder)
Click OK
Click Next

The 1.0.2 that I downloaded from Arduino is using avrdude 5.11 and supports "wiring"

Yes, there is already an issue opened and the developers said they are working on it:
https://github.com/arduino/Arduino/issues/1114

Assuming ignore usb hardware serial number is set:

If you had two USB ports on the system, you would need to install the drivers for each port.

After that, then any UNO should work in any of those two ports without further driver installation.

The change to "wiring" added in 1.0.2 to address an upload issue, see here for details: https://github.com/arduino/Arduino/commit/d83543cff15d8a1f4623b1e2babc6c2f4a867815

Here is some more background information:
http://arduino.cc/forum/index.php/topic,90826.msg686935.html#msg686935

Here is an article that may help you solve your problem. It is a setting to tell Windows to ignore the serial number and treat all of the devices as the same device:
http://www.ftdichip.com/Support/Knowledgebase/index.html?ignorehardwareserialnumber.htm

Note: The solution in the FTDI article will work for UNO and any other USB device, just use the UNO VID and PID.

[Drivers]

The UNO does not use the FTDI chip...

Follow the steps here to disable driver signature enforcement on Win8:
http://arduino.cc/forum/index.php/topic,94651.msg727588.html#msg727588

Then follow these steps to install the UNO drivers:

Right click the Unknown Device in Device Manager
Select Update Driver Software
Select Browse my computer for software
Click Browse button
Select the Drivers folder under the location of your Arduino software installation. (Do not select the FTDI folder inside the Drivers folder)
Click OK
Click Next