Can I run the GenTrn program on Windows with a variable length extract file?

Yes, as long as you specify the maximum extract record length in your INI file:

< TrnFile >
MaxExtRecLen = XXX
Note   Make sure your transaction search mask and key information do not occur beyond the length of the shortest line. Otherwise, the system might assume a new transaction begins at the wrong point.

For instance:

< ExtractKeyField >
SearchMask = 11,HEADERREC
Key = 100,7

If you have a line that will be shorter than 107 characters (offset 100 for length 7), you will get a new transaction starting at that row.