For Custom Shop:
It is a custom shop; you open up significantly more options than option order; of course you pay for this privilege. I have read that a CS Bass automatically adds ~$1000 upcharge. However, you also open up things like pickup placement changes, nicer woods/finishes, changing how controls are mounted etc. I do not believe they will resurrect a no longer existing model for you.
On the G&L history question several links posted for you below. At a high level...
L-1000 was first, followed by L2000, Original versions of SB1/SB2 (they were not split coil P basses)
L2500 was introduced years after the L2000. G&L did not make a 5 string bass until the L5000 in 1988 (narrow string spacing MFD Z coil pickup). That was followed by the L5500 (EMG Pickups) and finally the L2500.
The big improvements with G&Ls are MFD Pickups (they are hot and have their own sound) and the passive treble/bass cut controls. Several other features that are unique to G&L, but those are the big two that make it a G&L IMO. Noting that G&L does have several basses without either of these features.
Links
[Invalid or Expired Link Removed] - Registry of models including highlights for some limited ones
GGJaguar - Photos/descriptions of several models
History available online - there were a few good books published, but this is the only online source I have found.