I'm not familiar with Hijack This!, but I may be able to help you. I used to use McAfee Security, but I noticed some of the same probelms your having were happening to me. Slowing down, errors, applications not starting until shutdown, and other symptoms that my computer was being infested by viruses & spyware. I deleted McAfee and I was supprised to find that my computer acutally ran better with McAfee GONE! I knew that if I didn't get any protection soon my computer wouldn't last. After several hours of googleing I found software that has been good even till this day (and it's free).
I use AVG Antivirus which might not be the best antivirus software out there, but it was far better to me than McAfee. I detected over 60 viruses on the first scan that McAfee was missing.
I use Spybot Search and Destroy to get rid of spyware. It does a superb job. I found well over 50 cases of spyware on my computer.
I use Zone Alarm firewall instead of the McAfee firewall. I didn't notice a sharp increase in the number of blocked attacks; the numbers were about the same per month. I didn't notice that it wasn't anywhere near as draining on my system preformance when it was running.
When possable I use Mozilla Firefox instead of Internet Explorer. I find Mozilla Firefox loading pages faster than Internet Explorer. I've also hear from some friends that Firefox attracts fewer viruses and spyware than Interent Explorer.
Most people don't think about this when protecting their computer, but old spyware and viruses that once were destroying your computer can sometimes realy mess with your registry keys. Even legitimate programs that weren't spyware or virus infested may have accidentaly been uninstalled incorrectly. Easy Cleaner is free software that will get your computer up to speed, about 20% faster up to speed.
The above claims were not in any attempt to shoot down or raise up any company or their software. These claims were only descibing my personal experiences with different software. I will not be responsible if any of the above software damages your computer.