Hello Devdatta,

I added the option --extra-inputs=file1,file2,... to the farmout 
scripts.  Condor will transfer these files from whatever path you 
specify (could be /scratch or /afs) to the working directory where the 
job runs on the worker node.  Since the files will appear in the working 
directory, rather than at the original path, you would probably not want 
to specify any path to these files in the CMSSW config file.  In other 
words, the job should assume that these files will be present in the 
current working directory when it runs.

Let me know if the above description is confusing or if it doesn't solve 
your problem.

--Dan