That's good. Yes, probably unrelated.

Don't forget to enable your anti-virus again.

You can go ahead and delete DDS and its two logs.

It's up to you whether or not you want to keep Hijackthis.

It's time for some housekeeping. Because the tools we used to scan the computer, as well as tools to delete files and folders, are no longer needed, they should be removed, along with the folders created by these tools.
(If you named Combofix.exe something else when you downloaded it, make sure you rename it back to Combofix.exe before uninstalling it)

* Click Start then Run
Copy and paste next command in the field:

ComboFix /Uninstall

Make sure there's a space between Combofix and / Then hit enter.

This will remove ComboFix, run some cleanup procedures, and flush System Restore, thus creating a clean Restore Point.

Check to be sure a new Restore Point was created. If not, do it manually by turning off SR and turning it on again as follows:

To turn off Windows Vista System Restore:

1. Click Start.
2. Right-click the Computer icon, and then click Properties.
3. Click on System Protection under the Tasks column on the left side
4. Click on Continue on the "User Account Control" window that pops up
5. Under the System Protection tab, find Available Disks
6. Uncheck the box for any drive you wish to disable system restore on
7. When turning off System Restore, the existing restore points will be deleted. Click "Turn System Restore Off" on the popup window to do this.
8. Click OK
9. When you have finished, restart the computer and follow the instructions in the next section to turn on System Restore.

To turn on Windows Vista System Restore:

1. Click Start.
2. Right-click the Computer icon, and then click Properties.
3. Click on System Protection under the Tasks column on the left side
4. Click on Continue on the "User Account Control" window that pops up
5. Under the System Protection tab, find Available Disks
6. Place a checkmark in the box for any drive you wish to enable System Restore on
7. Click OK

Here is my standard list of simple steps that you can take to reduce the chance of infection in the future.

If you have used Malwarebytes' Anti-Malware as part of your cleaning procedures, keep it updated and use it to scan every so often for malware, or upgrade to the paid version for realtime scanning and auto updating.

The following suggestions are general prevention and are not customized for your computer. You may have already taken some of these steps, and depending on your current security, you may not need to implement all of these:

1. Visit Microsoft Update: Make sure that you have all the Critical Updates recommended for your operating system, Office, and IE. The first defense against infection is a properly patched OS from Microsoft Update at update.microsoft.com. More info HERE.

2. Please use a firewall and realtime anti-virus. Keep the anti-virus software and firewall software up to date.

3.You might consider installing Mozilla / Firefox.
http://www.mozilla.com/en-US/

4. Do not use file sharing. Even the safest P2P file sharing programs that do not contain bundled spyware, still expose you to risks because of the very nature of the P2P file sharing process. By default, most P2P file sharing programs are configured to automatically launch at startup. They are also configured to allow other P2P users on the same network open access to a shared directory on your computer. The reason for this is simple. File sharing relies on its members giving and gaining unfettered access to computers across the P2P network. However, this practice can make you vulnerable to data and identity theft. Even if you change those risky default settings to a safer configuration, the act of downloading files from an anonymous source greatly increases your exposure to infection. That is because the files you are downloading may actually contain a disguised threat. Many very malicious worms and trojans, such as the Storm Worm, target and spread across P2P files sharing networks because of their known vulnerabilities.

5. Before using or purchasing any Spyware/Malware protection/removal program, always check the following Rogue/Suspect Spyware Lists. http://www.spywarewarrior.com/rogue_anti-spyware.htm http://www.malwarebytes.org/database.php

6. If you have not already done so, you might want to install CCleaner and run it in each user's profile: http://www.ccleaner.com/ ** UNcheck the option to install the Yahoo toolbar that is checked by default for the Standard version, or download the toolbar-free versions (Slim or Basic) when given the option for those.

7. Web Of Trust , uses colored alerts to warn about risky websites warns you about risky websites that try to scam visitors, deliver malware or send spam. Protect your computer against online threats by using WOT as your front-line layer of protection when browsing or searching in unfamiliar territory. WOT's color-coded icons show you ratings for 21 million websites, helping you avoid the dangerous sites:

• Red for Warning = STOP
• Yellow for Use Caution
• Green for Safe
• Grey for Unknown

There is a Web Of Trust version for Firefox as well.

8. You might consider installing SpywareBlaster: http://www.javacoolsoftware.com/spywareblaster.html
It will:
Prevent the installation of ActiveX-based spyware, adware, browser hijackers, dialers, and other potentially unwanted software.
Block spyware/tracking cookies in Internet Explorer and Mozilla Firefox.
Restrict the actions of potentially unwanted sites in Internet Explorer.
Tutorial here:http://www.bleepingcomputer.com/forums/tutorial49.html
Periodically check for updates

9. You might want to install Winpatrol. Winpatrol is heuristic protection program, meaning it looks for patterns in codes that work like malware. It also takes a snapshot of your system's critical resources and alerts you to any changes that may occur without you knowing. You can read more about Winpatrol's features here.
Download a free copy of Winpatrol or use the Plus version for more features.
You can read Winpatrol's FAQ if you run into problems.

10. Here are some helpful articles:
How did I get infected?  HERE

  I'm not pulling your leg, honest?
by Sandi Hardmeier  HERE

Let us know if we have not resolved your problem. Otherwise, you are good to go.
Happy and Safe Surfing!

Are these symptoms from before we cleaned, or after?

They started up after we cleaned, but they were problems that had occured 1) in the past,  and 2) prior to the search engine issue.

However, after restarting the computer a few times, word, and my pdfviewer program are back working.. Certainly appears that the problems are unrelated

thanks! Looks like the problem is fixed