Arduino Yun 32U4 Bootloader corrupt

Hello all,
My Yun recently started not uploading sketches, and after reading through other material, I think my boot loader has become corrupt; I get an error that the programmer is not in sync, and I have gone through the troubleshooting guide to isolate the problem.(Pin 13 LED turns on as well) After coming to this conclusion, is there anything special I need to know about re-flashing the bootloader on a Yun? Also, I have problems resetting the wifi on the linux side of the board. Are these problems related?

Sorry it has taken a while for any one to respond. Probably the way the question was asked was a bit busy.

Lets start with getting wifi up if its possible.

1 Hold the wlan, let go before 30 sec

2 connect to the yun directly with your pc

3 Go to 192.168.240.1 in the address bar

When you follow these steps what happens? Ive gone thru a bit of fustration with this thing too.