How about making your own folder next to assets and place your files in there? Next will be a path issue and while it could take a while to go through all files, if you can get it to work with one file, you should be able to get it to work with all files. Something like adding a ..\ prefix to the paths. CvXMLLoadUtilitySet.cpp contains the paths to the xml files, in case you want to move those too. The path to text xml files is also somewhere in the DLL, though I can't remember where offhand.
I did some experimentation at some point and it seems to spend way longer on dds and nif files than say xml files. Moving those two file types would likely make a huge difference and then you can skip the rest.
I have no idea why it has to spend ages indexing because apparently if you pack the files, then indexing is instant or not done. Packing the files has memory sideeffects though and there are examples of computers crashing from reading packed files while they managed unpacked files just fine.