A lot of the responses to this question involved looking at the SQL analyzer.
I reread my question and I realized that I omitted the fact that it is pulling the entire file. I do not have access to the program source but apparently it is doing a "select * from file". No where clause, no order by clause. Just a full file pull in whatever order the IBMi hands it to them.
I have gotten nowhere in the discussion on this. The team receiving the data doesn't see a problem with our IBMi CPU being over 100% for hours at a time and therefore does not want to change anything. I'm dropping it for now. We will see if someone listens to the problem when holiday peak shows up and SLAs are missed because the machine is overworked pushing this data to the other server. :(
Thanks everyone for your thoughts.
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