Just unzip the MODX package (make sure it's exactly the same version) on you local machine and transfer the setup directory to the modx root directory on the remote.
Since you don't have a setup directory, you won't be overwriting anything in the transfer.
When you run Setup, MODX will recognize that you have an install and will run Setup in upgrade mode (don't proceed if the "update existing" box isn't checked), so you won't lose any of your work. The only thing that should change is the path strings, which may solve your problem.
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PLEASE, PLEASE specify the version of MODX you are using.
MODX info for everyone:
http://bobsguides.com/modx.html