Mac Pro :: Does Spotlight Begin To Re-index Drives After Each Startup?

Three days ago I was browsing the web when my cursor evidently brushed over an ad for MacKeeper. In a few seconds MacKeeper had downloaded itself without asking and taken over Safari. Since I don't like thuggish behavior in people or in software, as soon as I regained control of Safari I moved MacKeeper to the trash and did a "Secure Empty Trash." I then aimed Intego's Virus Barrier at the Downloads folder and it found nothing questionable. I checked out various webpages where people describe how to rid your computer of MacKeeper if you've installed it - - I didn't install it, but I checked in all the recommended places and found nothing visible. However whether it is a coincidence or there is a causal relation immediately after this incident, Spotlight began to re-index my two internal hard drives - - estimating first that it would take 3 days, then 7 days to index them. I wrote about this on another thread and received the following advice: 

"Spotlight's probably in a wobble. A few things you could do: 

1. Tell Spotlight to start again. Open Terminal (Applications > Utilities > Terminal.app) and copy/paste this command: sudo mdutil -E /

Press 'return'. You'll be asked for your password, which will not echo when you type it, so type carefully. 

Give Spotlight a few minutes then check on its progress, does it look like it's going to complete in a reasonable amount of time? If the problem persists 

2. Restart your Mac in Safe mode and log in to your account.

This'll take a while. When it's finished, immediately restart and log in normally and check on Spotlight again." 

I performed the first step. After a few minutes Spotlight estimated that it would complete indexing in 20 minutes. Over the next few hours it continued to increase its estimates to an ever larger number of hours. 

Then I performed the second step. After completing it Spotlight's estimate was that it would take several days. 

Eventually I performed the first step again and the same sequence of increasing estimates occurred.  

I left the computer on overnight and by morning Spotlight estimated it would take 35 hours to complete indexing of my drives. 

Later on I turned the computer off. When I started it up again Spotlight had started once again to re-index my drives and now estimates it will take 5 days.  

None of this behavior had occurred before the mishap with MacKeeper. Since I have a recent clone of the startup drive that was made before this incident it seems possible that I could zero out my internal startup drive after saving any files that have changed to a DVD, use Virus Barrier to check if there is anything questionable present in the folder in which they are located and then clone the data from the backup drive back to the newly formatted internal hard drive. However I would rather not have to do this, so I would be most grateful for any less extreme suggestions. 

Info:
Mac Pro (Early 2009), Mac OS X (10.7.4), 24GB RAM/MOTU 2408 mk3 audio interface