Yes, it is possible to put the input file name into the name of the export using DataPump, as well as useful things like timestamps, job log numbers and so on.
You don't need to define multiple projects for each file - as long as the files are of the same structure, and so can be processed using the same model, then in DataPump you can define the input mask using a wildcard.
So one process could handle all the files of the form DD9001P*.txt, and the export could be defined to create .xls, so DataPump would create DD9002P_1123_2013-09-30.xls, ,DD9002P_142_2008-11-20.xls etc.
For the more complex cases it would be helpful to get more details - is it possible for you to save the job log of that process and to email me that as an XML file?
Could you please describe how to set the export so that the file is named appropriately? Like .xls, as you mentioned above? Is it a function you put in the export properties dialog?
It appears that there are macros in the export properties dialog that allow for adding the input file names as well as dates and timestamps. There is a little down arrow next to the box where you type the name of the file to be exported.