I think you should close the Arduino IDE and just try using AVRDUDE + Pololu USB AVR Programmer to flash the bootloader on to the Arduino.
First of all, have you located the HEX file for the bootloader that you want to burn on to your ATmega328?
Secondly, have you determined what COM port your programmer is on? Please unplug your programmer, plug it back in, and then look your Device Manager and tell me all of the entries you see under "Ports (COM & LPT)". The one that is labeled "Pololu USB AVR Programmer Programming Port" is the COM port you should be using
Please try to burn the bootloader by opening a Command Prompt and typing something like
avrdude -p m328p -P COM2 -c avrispv2 -e -U flash:w:bootloader.hex
You should replace COM2 with the name of programming port as shown in your Device Manager and replace "bootloader.hex" with the name/path of the bootloader HEX file that you want to burn.
If that does not work, please post the command you ran and the entire output of avrdude here. If the red LED on the programmer turns on then try running the Pololu USB AVR Configuration Utility (which is included with the drivers) to find out what the error is, and use that same program to tell us what ISP frequency the programmer is configured to use.