In the professional version you can pre-set the actions to be taken upon detection so the scan would continue uninterrupted. The Home version requires interactive action selection for each detection (as you found), that is what Tech is saying in a round about way, but I believe he may have thought you have the Pro version.
Yes, a manual scan is an on-demand scan. Deletion isn’t really a good first option (you have none left), ‘first do no harm’ don’t delete, send virus to the chest and investigate.
If you at some point checked the don’t show this window again (and don’t remember) you should have been presented with a list of detections at the end of the scan, but again it shouldn’t have taken autonomous action to delete. So that is a mystery as you say you are sure you didn’t don’t show (ask) again, unless it is just summarising the scan and you had taken action to delete the file.
Archive (zip, etc.) files are by their nature are inert, you need to extract the files and then you have to run them to be a threat. Long before that happens avast’s Standard Shield should have scanned them and before an executable is run that is scanned. Thorough is also by its design very thorough and perhaps a little overkill for routine use, were a Standard scan without archives should be adequate.
I have only ever done a through scan with archives once shortly after installation just to ensure a clean start state, but with XP for example avast will do a boot-time scan after installation if you select it, this I believe will be quicker and reasonably effective. Like everything in life things are a compromise.
Over time this interactive decision requirement of the home version will become less of an issue, as the resident, on-access scanners are designed to intercept infection before it gets into your system. However given the size of your data, even a Standard Scan without archives will take some time, but no where near 3 days.
If your primary HDD only has 15% free space that could also be hampering you (and the scan) as the archive files are extracted to a temp folder C:\Documents and Settings\UserName\Local Settings\Temp_avast4_. There are those that will say you need to either upgrade your HDD or archive stuff off to DVD/external HDD so that you have at least 20% free space. The amount of free space can also have an effect on the windows defrag (if you use it) where it may say there is insufficient free space to defrag.
Welcome to the forums.