Personally I would take the direct IND PHX flight Wed AM (FDX 1755) it shows at 2:55 am and gets you there by 6. Any of the Tue night EWR to IND flts will get you there in time. It looks to me like competition for the seats through IND is much less. If possible see if EWR Security will tag your bag straight through, but you will probably have to drag the bag anyways in IND.

For the FDX guys our JS system seems to ignore some flights when you ask to JS on multiple legs, particularly if your request spans multiple calendar days. It is best to look at separate pairings.