You need two different shipyards, since frigate/cruisers cannot be built from capital yards and vice-versa.
It is possible to remove metal/crystal extractors, you just have to remove metal/crystal costs from everything so players don't have to use the Black Market to purchase metal/crystal.
They will probably have to use non-canon material for some stuff since the Vasudans and Shivans have no Starbases in canon, and those things are powerful in Entrenchment with lots of support abilities (fighter hangars, preventing loss of planetary control, repair and resupply for nearby ships). Considering in the FS1 mod even the scout frigates carry fighters, a Starbase will potentially have massive numbers of them, and Entrenchment allows four fighter types per carrier now so an Arcadia could have everything from Perseii to Boanerges backed up by hangar defense structures and their fighters.