I would also suggest that this is probably a bad idea, because it doesn't sound like a good architecture for an actual app. Rather, it sounds like what you would do when you're developing in LV, so maybe that's what your end users should be doing. But maybe you really do need this, so let's crack on.
My first suggestion would be to use a subpanel. After the user selects the VI, you load the VI, put it in a subpanel, hide all the indicators and run the VI when the user presses a run button. That way, the user simply inputs the values directly on the FP.
A second option might be to use an existing framework for running VIs, like VI Tester or the Unit Test Framework. I have no real experience with them, so I don't know if that will work for you.
A third option would be to try going down the way you're going. You can use the flattened values, because as you see, they're not designed for readability, so you'll need something that converts the values. You can see examples of this type of conversion in the OpenG or MGI variant VIs, and what you will find is that it's hard coded - you need to have a specific case for every basic data type you support. There's special code to recursively handle arrays and clusters, but that just means the string the user builds will have to be in a very specific format.
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