I like the concept of you just can't switch yards between projects willy-nilly, but I think the concept of tooling up is at least a little outdated.
I'm a fan of shows like Modern Marvels and Build it Bigger (which are especially cool in HD) and the new catch phrase seems to be 'Design-Build'.
The concept behind this is that the workers start building some parts of the ship before every single bolt and cable run is laidout. Assisted by 'walk through CAD' this seems to work very well.
To me the concept of tooling up appllies to large scale manufacturing in the 60's-90's where the workers would first make the rigs to make the parts to make the ship (or plane - I saw this myself at Boeing in the late 80's).
With current computer controled equipment this is less of a factor - tooling up pretty much just requires downloading the CAD file of a part into the right tool (cutter, welder etc.) and off you go.
Considering all of this I think that some first of class surcharge is appropriate but that taking about 1/2 as long as a ship takes to build to be ready to start building is excessive. (I think that if any current commercial shipyards did this they would be out of business very quickly.)
My thought would be about a 120% time for the first of any ship and maybe 105% material cost - which in aurora is significant. These could even start higher and be researched down like most everything else, call it racial Design Efficency.
This would only apply to the first one ever and others could be started as soon as the first got to 'normal time' remaining. Each shipyard could then keep a record of the procedures and could switch to another class, then switch back ad a very low (say 105% time only) or no cost.
The question of trading these between shipyards might depend on gonvermental or industrial factors, ie a comunist govt all the yards are owned by the state so transfer is automatic, while in a corporate each corp protects its own designs and govt contracts).
Mike