Thanks for the screenshots. They contain the answers to what you have observed.
10,000+ lines in the scan report indicates a cluttered registry. Also, Power Tools builds the scan report in memory (and virtual storage). Those two facts explain both the 10 to 12 minute scan time and the CPU spikes.
Once you clean out the "errors," Registry Cleaner should run in less than a minute without the long CPU spikes.
It sounds like you are proceeding slowly and cautiously. That is good with such a large list. No registry cleaner is perfect, so a careful examination is appropriate.
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Here's a shortcut you may want to try. It may reduce the RC list to a more manageable size:
1. Make sure you have Power Tools backup turned on in Settings
2. Run Registry Finder with these settings:
Search words -- \userassist
Search by date -- leave it unchecked
Search method -- check normal
Options -- uncheck everything except "HKEY_CURRENT_USER" and "Analyze key names" and "Analyze value names"
Ignore words -- HRZR_ and \Explorer\UserAssist\
The resulting list will contain a line for this key: HKCU\Soft\MSoft\Win\CurVer\Explorer\UserAssist\ -- it will probably be the only line
3. Click the line's check box and click Remove
4. Impact? You will lose for a time the list of frequently used programs that appears when you click the windows Start button (assuming you have that feature turned on). Not to worry -- windows will start to rebuild it the next time you reboot and use the PC for a while.
5. Run Registry Cleaner and let me know what difference that made in the run time and error count.
6. First, you may want to read this Forum thread which (eventually) discusses UserAssist.