You can drop in an '04 through '06 E150 rear axle. Some '07's also, but that was the transition year where they started building them with Dana 60's. My guess is Wagons all got the D60, but early cargos still had the Ford axle.
Also, have you made sure the brake show adjusters are working? You might get some improvement just manually adjusting the star wheels.
Up front, you might be limited to better pads. I'm really happy with the Napa Ultra Premium pads. Anything ceramic is worse when cold. Tried it once, and almost went through the first stop sign by my house on a cold morning.
2000 E450 dually V10 wagon