When I do the inboard joint reboot on my civic, the factory manual specifies an uncompressed length that the shaft has to be after assembly. Before sealing the inboard clamp, I slide a pick under the boot for a vent, and pull the shaft out of the joint to that length, then remove the pick and clamp the boot to trap the air needed to provide the force that keeps the joint from popping out of the transmission while in use. I haven't had the pleasure yet on the Vibe, but I was rebooting the civic shafts about every six years. I inspected them every oil change and when they started showing cracks about half the thickness of the boot, I'd invest the $12 on new boots and grease instead of waiting for the boot to completely blow out and get destroyed. Over 200k on the original shafts, as long as the boots stay intact, they last forever.
That said, I believe you were given the incorrect shafts if they are that much shorter, either they were boxed incorrectly or pulled incorrectly. Take your measurements with you and exchange them for shafts that match what you took out. If you can't return them, consider just swapping the new joints onto your original shaft.