Ok, I think we need to wait for KP to take a look and see if he can move the files that you've uploaded already to where they should be.
At the very least he can restore the directory structure to what it should be so that we have a blank canvas.
I think the problem here is things have got so confused that we don't have a common starting point/frame of reference.
Once the online directory structure is sorted/straightened it should be possible to talk you through the upload a step at a time. I'll open up Filezailla on my machine and walk you through each step of the process, in theory we should both see the same screens (albeit I won't be able to see your directories/files but that shouldn't be a problem).
Once you've done it once you should be able to repeat the process.
I need to go out now though so it will have to be tomorrow night / later tonight.
There is one other alternative, but that would rely on KP sorting the structure of the site first, and then you getting someone else to upload the files for you. Not a great solution as they would need your password and you would still need to get the files to them.
I'll check back a bit later and see if there have been any developments.
I honestly think that if you can get this cracked you will see that it's money well spent
