You can use the latest revision of Rathena, and use the most stable client as far as I know. Which is 2013-07-03aRagexe.exe. as for your question about the starting point. By default. The Rathena is renewal, you can change it in trunk/src/config/renewal.h
Uncomment all the renewal lines to switch to pre-renewal. and for your last question. You have to do it manually, all of the quest,maps, npcs, are enabled up to the latest episode as possible. You can disable all of those maps, quest, npc one by one.