When the the Fender Passport 250 is plugged into the computer through the stereo out, there is feedback/buzz in addition to the sounds the microphones pick up, even when the mikes are off.

wow.....um, buy another

A shorted speaker cable could cause this... however, what you do is to replace the fuse BUT wire a 150 Watt lamp in series with the power input... This acts as a resetable fuse for testing. If the lamp stays lit, you still have a failure.

Make sure the passport speakers are NOT where the guitar can hear them... they need to be toward the audience from where you are. Also do NOT boost the high end frequencies with the EQ. That guitar probably has a hot pickup subject to ambient sound. Beyond this, you might have to use one of the feedback destroyers. If you are using monitors, take the guitar out of them.

Best way is to use a 1/8 TRS (stereo) to 1/4 TRS (stereo) cable from the PC into the Stereo 1/4 inch jacks right below the RCA stereo input jacks.

TRS stands for tip-ring-sleeve which means the jacks have the extra "ring" over a mono jack.

1st connect the digitech vogalist
(Line Out L/R)
output to one (line input) from boss br 900 and the boss (line output) to the passport (stereo input) use a high quality cables, to supress noise efect, on output.

The manual is here if you don't have one:http://www.fender.com/support/manuals/pdfs/manuals_elec/fenderaudio/PassportP250.pdf Have a look at page 9 and read the VIP Channel 1 only section. It will explain the solution to your problem and the settings to overcome it. Please let me know if this helps.

Plug your keyboard into a line input. Run a cable from the stereo out put jack into a separate amplifier with a speaker e.g. a self contained powered monitor.

I have one that is doing the exact same thing. It's at a Fender
Authorized Service Center now. Hopefully dude can find the
problem. Fender says there is a 5 year warranty on it, so I
expect them to make good on their promise. Did you get
yours fixed?

It seems like the speaker jack tip needs cleaning, or the contact has become bent away from the connector and needs to be re-aligned.  The Passport is a portable system, so after years of plugging and unplugging the speaker jacks may be worn.  Try using the "Stereo 2" connectors. You can also try cleaning the jack with electrical contact cleaner, and. a cotton swab. 

If you're still in need of a manual for your Fender Passport P-250 it can be found at:
http://www.fender.com/support/manuals/pdfs/manuals_elec/fenderaudio/PassportP250.pdf

Good luck!