It sounds like your setup is good. The uploaded files that are complete but aren't at 100% just means they got the rest of the file from someone else. Most of the time when you d/load a file, you get it from more than one host and that's what's happening there. The percentage shown is just the percent of the file they got from you.

I have my upload bandwidth set so I give about 5KB/s per upload slot. So having two slots open sounds about right. If you make it too high, you'll have a lot of people queued but the uploads will be too slow.

Not sure what to do about bearshare lite. I imagine they are sharing files too. So blocking their ip addresses might not be a good idea.

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