That’s over 2Kg weight difference between the pro-spec and yours.
Shimano running gear is generally heavier than the equivilant in Campag or SRAM. That might account for a few hundred grammes there.
Allowing for a few hundred grammes on the finishing kit.
Which means you have some very heavy wheels (relative to the pro-spec bike)?
Incidently, Zipp 404s apparently weigh just under 1500g.