Ivan was able to help me with this one. Next time I will have more experience to figure this out on my own. For the new to EDI config file folks, here is what needed to change for my scenario:
At the end of the ISA, the medi segment needed moving
<medi:field xmltag="ISA14 I14 Acknowledgement Requested" />
<medi:field xmltag="ISA15 I15 Test Indicator" />
<medi:field xmltag="ISA16 I16 Subelement Separator" />
--xx--xx </medi:segment> ---this needed to move to under IEA at the very end of the file
<medi:segment segcode="IEA" xmltag="Interchange Trailer">
<medi:field xmltag="IEA01 I16 Number of Included Functional Groups" />
<medi:field xmltag="IEA02 I12 Interchange Control Number" />
</medi:segment>
</medi:segment>
</medi:segments> ---moved to under IEA
</medi:edimap>
I had tried this at some point, but it did not occur to me that I would need to change the DTMs scattered throughout the file, because they were in their own segments. After the first DTM01, DTM02, I changed the rest to DTM03, DTM04, etc.
Thank you Ivan! It was taking a lot of time to change, test, change, test and we were under a time constraint.