Yep.. stock transmission, stock flywheel, stock FPR and stock fuel pump!!
You can upgrade but its not necessary. In regards to the flywheel/clutch combo.. I'm very happy with my ACT setup, a lot of people on this board are running clutch masters and spec clutches.
ebay intercoolers are fine. tons of people are running the turbo xs ebay units and they haven't had any complaints. i'm running an old isuzu npr intercooler, I would love to upgrade personally to a $90 ebay unit lol