What product suite/tool are you migrating from to webMethods EDI?
Also SAG provides some EDI migration utilities that might be useful to you especially migrating maps (Gentran/GIS or Harbinger TLE to name few)…Did you talk to their Rep/support?
Ofcourse migration would be a painful/risk roadmap when dealing with complex coded/custom mapping objects and deals with lot of end to end mineute testing:
HTH,
RMG