If I understand what you are trying to do, I think you'll need to create your custom MIDConfig.parse (modify the existing one and save as a new name) file and then try this:

sfffile -s GSMID roche454_trimmed.sff -mcf /locationof/customMIDConfig.parse sff/roche454.sff

This would sort your "roche454.sff" into separate files by GSMID located in "customMIDConfig.parse" (or whatever you wanted to call it.

You write that the mid.lst file is in GSMID format. Then you should use the -mcf flag instead of the -e flag. Also, please make sure the file adheres to the following structure:

mid_set_name
{
     mid = "name1", "ACGT", 1;
     mid = "name2", "CGTA", 1;
     mid = "name3", "GTAC", 1;
}

The number at the end is the maximum number of allowed errors in the MID sequence.