Spotlight not working...other important systems compromised.

Hello, I have a slightly older MacBook. It was purchased when leopard was out, but has been upgraded to lion, with ram added.

Had no problems with the OS until I installed the seagate diagnostics software about a week ago at their recommendation.

During the install, the computer hung during the shutdown of the mandatory restart. It took me a pram reset to get the machine to start up again. Since then, the following has been a problem:

-Spotlight has no index and won't search.

-The computer will not shut down, have to pull the plug.

-Finale (which uses java runtime) doesn't work, and the auto install of java run time won't go in.

-Software update starts, but the percentage bar freezes after a moment.

I have run the system restore partition, which went in okay, but did not change anything. I have also followed the steps to uninstall the seagate diagnostic software. However the problem still persists. I'm guessing there is some sort of shut down script that is hanging the system, and preventing indexing from happening which prevents all of these other processes from happening. Does anyone have any ideas for what to do next?

Thanks,

Chris Roode