Well first off Vista is notorious for not working with certain audio programs do to vista using a new audio architecture. So I would research on the software you installed and ensure that it has vista support and any surrounding issues.

Hijack this is an analyzer to scan your computer for possible hijacks and maleware bytes performs a similar operation.

Yes your virus scanner can miss viruses. One virus scanner cannot detect every possible virus out there.

To my knowledge torrents can have viruses and often do.

To protect against viruses and such use a virus scanner as you are doing, keep it updated, and download from trusted sources.

ABSOLUTELY. P2P is one of the most common ways to infect a computer AND to infect it very dangerously. Your anti-virus program won't see them because much of the time they AREN'T viruses but trojans, two very different things.
Uninstall whatever it was that caused the computer to not respond.

TURN OFF the Bittorent Program so that it is NOT running all the time.
I would highly recommend doing this:
lease Download ATF-Cleaner.exe by Atribune(Windows XP, 2K, 2003 & Vista ONLY)

• You can put ATF-Cleaner on your Desktop for easy access.
RUN ATF-Cleaner.exe.

-- Click on ATF-Cleaner to run it
-- Where it says Select Files To Delete, Check the Select All Option
-- Click Empty Selected > OK

If you use Firefox browser, do this also:

* Click Firefox at the top and choose Select All from the list.
* Click the Empty Selected button.
* NOTE : If you would like to keep your saved passwords, click No at the prompt.
Next do the following:
Please download Malwarebytes' Anti-Malware (MBA-M) to your Desktop.

* DoubleClick mbam-setup.exe and follow the prompts to install MBA-M.
* Be sure a checkmark is placed next to Update Malwarebytes' Anti-Malware and Launch Malwarebytes' Anti-Malware, then click Finish.
* If an update is found, it will download and install the latest version.
* Once the program has loaded, select Perform full scan, then click Scan.
* When the scan is complete, click OK, then Show Results to view the results.
* Be sure that everything is checked, and click Remove Selected.
* When MBA-M finishes, Notepad will open with the log. Please save it where you can find it easily. The log can also be opened by going to Start > All Programs > Malwarebytes' Anti-Malware > Logs > log-date.txt.

Reboot the computer.

Next, download HiJackThis and run a Full system scan with it and save the log. Post back here with both the MBA-M log and the HiJackThis log.
I would bet you money that this first computer is also loaded with malware due to P2P file sharing.
This is a very dangerous activity. Besides getting all these FREE programs you very likely are loading the computer with Trojans which then connect to the internet ON THEIR OWN and open the door to the world all of your private informations...name, address, telephone number, BANK ACCOUNT numbers, Credit Card numbers..before long it is not only the computer which can be wiped out, you can be wiped out.