What you are asking are very good questions. These are what are known as forum etiquette questions. I'll do my very best to answer them for you.
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Is it against protocol to insert these questions into the topic thread I am reading, kind of like a 'er, excuse me, I was wondering....'
This is known as hijacking a thread, and not considered good etiquette. The best thing to do is create a new topic for your specific question and link to the topic that prompted your question. This way each person gets individualized attention and it lessens the chance the subject matter will stray off course from the original posters issue.
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Must I break my list into topic areas, or can I post em all in one post? (f'rinstance, one is about firefox, one is about the task manager and one is about IE.
It is best to break down your questions into individual questions. Also keep in mind that you might want to tackle each issue separately so that you do not compound the problem in a 'related' as you say issue. Also it is much easier to follow just one thread at a time so as to not confuse you and or the multiple people trying to assist you.
I hope I have answered your questions. If not don't hesitate to ask. And best of luck in your forum adventures and tackling your issues.