Make sure you install to a completely new location, you can't be trying to write the same installs to the same location from two different sources. So basically, if your putting FPs downloading somewhere say c:\STO ...install the torrent version anywhere BUT there or you'll crash it.
It'll speed up over time. Thats how P2P/ torrents work.
Make sure you upload at a fair speed, but don't kill your connection...that might help you. So if you have a 512k upstream speed ..set your upload limit to like 40k tops. If you exceed that you'll likely start to lower the speed at which you can download .
A line needs to separate each once for the trackers to work. Perhaps if more of us add trackers that have the 100% it will be faster? I dunno, this is the first time I've ever added trackers to a torrent file.