Ever since i have been using iPhone Tunnel Suite it has worked for me,
each time i start a fresh restore, i install openSSH from cydia,
i make sure iTunes recognises my iphone,
then i double click iPhone Tunnel Suite, click on iPhone Tunnel
i then wait for it to load (it will come up with a bunch of writing and often say theres a security problem but just update the cache by clicking ok),
if u dont get to this step, restart iPhone Tunnel Suite, and if that doesnt fix it restart iTunes, and/or re-connect ya iphone. restarting ya iphone is the last option which i sometimes do.
then when you are able to get iPhone Tunnel to talk to your phone (with the code in the cmd like browser),
click WinSCP button (in the iPhone Tunnel Suite),
and just connect using the settings already provided.
that has always worked for me from day 1
sorry about the long explanations. i used to not like the short explanations when i was trying to learn from scratch, just made it more difficult to understand, hope this helps!