Have you talked to Napa, if it's not an exact fit then you have good reason to return it and question their cross reference.
Failing a return for the correct part, it would be important to identify the function of each fitting on both pump housings.
3/8 Should be , pump pressure to the engine on both.
5/16 on the original , should be the vent line to the emissions canister, and have the same function as one of the 2 on the replacement , but you need to know the correct fitting to hook to or you can put liquid fuel into the emissons cannister and ruin it.
The remaining fitting will be fuel return from the engine, and if you can't return the pump, things could get dicy here.
Are the lines on the M/H plastic ?
Can you post a picture of the fitting / elbows in question ?
99DSDP 3884, Freightliner, XC, CAT 3126B, 300 HP /ALLISON 3060
2000 Caravan toad, Remco & Blue Ox.