We were able to get the server to function by tuning a bit on the back end.
It takes about 22 seconds to recover the file from the FTP location (about 52 mb)
It takes about 70 seconds to write the file back out to the FTP location. (about 146 mb)
Since the file is a fixed length flat record the incoming adapter parses it to a schema (constructed in the process of defining the adapter instance)
That part seems reasonably fast and the transformation from the generated schema to the final output schema is almost instant.
Writing the results via FTP seems to be the biggest issue.