Sidequests

Wraiths
By defeating the 8 elemental Wraiths you gain the Wraith Nexus which opens a portal at the Mesosphere Arca on the Heyama continent.

EXP Farming
Early game you can fight Apex enemies south of Blue Creek. There is a very small appearance rate increase on the small forest patch up on the hill.

Late game the monsters in the Tenebrous Reef yield high EXP. Also, several of the bosses in the Heyama Stadium can be fought again for decent EXP, though most of them will have reduced EXP rewards.

PP Farming
Northeast of Blue Creek there is a small patch of forest up on a hill with Apextu enemies. You need the airship to reach it. They give huge amounts of PP but run after only a few turns. These enemies can also be radiated and fought in the Heyama Stadium, though they run away much quicker there.

Alternatively, Desert Dessert can be repeatedly fought in the Heyama Stadium for 20 PP per fight, which might be easier if the player has difficulty getting Apextu encounters.

Gold Farming
Gold Shield Bugs appear at 3 specific locations in Affliction. They drop large amounts of gold. They can also be radiated and fought in the Heyama Stadium but they become much more powerful.

Macroing
There are several locations in the game where you can set up a simple macro to repeatedly fight battles for EXP, PP, and Gold. The earliest is on Sandra's Ship below the deck. Use a program like "Auto Keyboard Presser" to keep killing rats automatically. You'll earn around 1000 PP per hour. After sidequests open up late game you can do this in the Heyama Stadium as well against most Ray battles. Some of the late bestiary entries yield high EXP.

Stat Building
Stat increasing items can be acquired through crafting using the "Junk" recipe book. Crafting requires a Dragon Jewel, which can be bought in Ellea, and various other ingredients. The junk can be traded to the Junk Shop at Lanariko village in Heyama.