Gelion I will be most happy to give any suggestions I can.
One thing civ 2 has over civ3 is the events ability. So you can create the major events of the RPGs.
As for start date, well I think thast unless you are going to fully create the factions with all their starting cities and units you should begin the game a lot earlier. I would suggest October 2077. Just after the nukes flew. That gives the civs time to fight the wastelands itself and possibly expand and get ready for the events from the RPGs.
For victories I would have a tech victory for the NCR, as they were non expansionist in the rpgs.
For the BOS I would have a tech victory only. They wanted knowledge, not conquest.
For the Ghouls I would have a tech victory. Since I think they would try to find a way to cure their condition or make themselves fertile again.
For the vault Confederation I would suggest tech or conquest victories. Also the Vault COnfed should have a higher starting tech base than the others. The same with the Enclave.
But since you can have only 7 civs, I would replace the Shi with the Unity. The supermutants were a BIG part of FO1. They would have a tech or conquest victory.
Cheers, Thorgrimm