Gene:
You are getting *WAY* too deep into this.  You need more help than I can provide on Clovertech.
To answer some of your questions:
No, you do not need the raw_hl7_ack  .  Pretty hard to send ACK via FTP.
The “^” in an lsearch  -regexe command i part of the regular expression we are searching for.  It constrains the search to the beginning of the string.  For eaxample ^MSH says I only want string that *START* with MSH.
You don’t need to escape all of those pipes when building the FTS, etc.  You could simply do something like:
        set fhs “FHS|^~\&|||||||||r”
Note that only the backslash itself is escaped 
I hope this helps