Regarding your questions:
1) Yes it is possible to import these files into a FlexPro database.
2) Basically you have to implement them in VBA (to be more specific: a COM add-in in any COM compatible language would also be possible).
The recommended way is to implement a custom import filter. Please take a look at the ImportFilter example located under
C:\Program Files\Weisang\FlexPro 7.0\Examples\VBA\Importfilter
This example gives a complete framework for an FlexPro import filter in VBA (it is fully documented in the online help). The example implements an import filter for a custom binary data format. I does so by re-using functionality of the binary import filter. In your case you could do something similar by re-using functionality of the text import filter. You just need to figure out the starting and ending positions of your data and you can construct a text import. This saves you the time of collecting all the values manually. The meta data can be collected and added in VBA and added as parameters to the datasets.
3) If you create the diagrams using VBA you can always assign the color in the creation step. For existing or manually created diagrams you could write a simple macro that does the color adjustment for you: First create a dictionary object which contains all the name to color mappings. Then create a makro which takes the active object (diagram), iterates over the curves and looks up the (Y-)dataset name of each curve in the color dictionary. Then update the color of the curve according to the map (or leave it alone if you don’t find the name). The macro can be executed either by connecting it to a toolbar button or you could take an event based approach (in an handler for ObjectModified for instance).