I can help you with this. One, they aren't overpowered so much as there is an elemental type for each enemy AND each character. That is, the main character is immune to fire (as that flaming thing) and absorbs fire (in female form). Therefore, if you want to train in female form, try to match up with a fire magic enemy. A good choice is either goblins or cerberus (hiding in a pot in the first inn). Also, the weapon/armour progression kinda extreme, and later equips may have you finding most of the too hard enemies way too easy. Second, for the "don't know the hell to be doing" to clear the first area, goto the mushroom and get struck by lightning, search the chests for keys, find the fire crest in the extended part of the grass (the lady to the right gives you a weird hint to its screen location as WEST), then go down and the trees should "burn" when you touch them, touch the fountain to open a cutscene, then notice the lone tree that didn't shed leaves when that earlier thunder struck, then grab the water drop from the fancy pedestal, and finally use it on the fire to the west. From there you can explore towns, but most of the puzzles in this game are roughly like this.

Okay, just in case I've missed anything.

Rune Key A: 1st room (can't leave without it)
B&C: 3rd room on lighted pillars (same)
D: 4th room lighted pillar trapped by puzzle (used for room 5)
E&F: store room in bars, knock down axe, and search bottom bed (if it still doesn't work, you're probably glitching)
Key to Ascendant Realm: Kill off one boss (ugh, currently only leviathan gives, I need to fix this in my next patch)
(Tell you what, I'll also make a secret ending ad, sorta like KH as apology)
Three Bosses: Kill them off (geh, if the other parts were too easy, I actually shudder whenver I test play this part), that touch the statue in the middle of the room. I'm changing the drop system to after battle, in case by some fluke it still doesn't drop.
Crystals: You should have all three gems by the time you enter this room. The sapphire is blue, ruby is red, and emerald is green. Place these in the appropriate circles, and activate the fourth stone to get teleported to the last boss. Good luck, this one is a epic length battle, and you can actually die (not that it matters anyway... since even the loss ending leads to victory is you have all characters).

K, getting cracking on the extra ending sequence.

Terraform is (correct me if I'm wrong) an Earth attack. I think Heaven and a few other places have rings or armor that relate to Earth. They should give some resistance. Other than that, try to find the weakness, keep whatever party members alive (Kenpo should survive) and bash away at until it falls.

SPOILER (don't read ahead if you actually want to solve these on your own).

Whew, Fox you picked a big one. The other party members can be gathered in the following manner, Kenpo is underground in the grove of those trees. Grab the first pice of the Hanatetsudai, experiment with jumping the river nearby. When you get to the bottom, hit the bit of steel there (it's a switch), to open a subcave in lake. Goto the northearth section, and look for a weird looking bit of driftwood. Actually, this is the second part of the Hanatetsudai. You can later goto the itemseller and get it forged. Then you jump into the water there, and head east until there is a hydra. If you can last five turns, defeat the hydra before that (or even pick a hidden third option to the hydra's questions) Kenpo shows up. I think this also gives you a Silver Key or something. Go to the third town, and there's MewMew (I think originally, she required a key to get to, but the current version doesn't seem to have it). Anyway, the cutscene after Kenpo should have opened up the way to Heaven. So go up there, defeat Gabriel, and there will be a choice. Pick the one that mentions freeing Heaven up or something, and Gabriel will join your party.

So that's two requirements for the secret ending just there. Might as well tell it outright.

3rd task, Get the Eternal Spring Flask: Goto the item maker, and ask for a Empty flask, and choose the option to fill it while you're there.

4th task, get Inuyasha's "back-scratcher" (really the Tetsusaiga, but it isn't used as a weapon here): Goto heaven and walk along the invisible platforms, make your way near Inuyasha, and keep asking him for his back scratcher. He'll quit after about 6 askings.

5th task, martial artist mastery: In the same screen, ask an angel whether you can do martial arts training, and when she asks if it's okay to leave your friends behind, say "Maybe?" (hidden third option in un-updated versions). Then go back down, and there's a new stairway at the base of Heaven. Talk to the shrine and you'll have a trippy meditation sequence after which you can equip the ultimate martial arts.

6th task, ultimate character: This replaces Ashley with another character who can cast all types of spells (I think it changes her immunities though). After getting Gabriel go back to the three choices (now only two) and choose, I want the Boxes of Orden. Choose the correct one (I may wish to save your game, as one choice destroys the world, and the other destroys you). The correct one changes you into a new character. You can undo this by the back scratcher or flask items listed above. But this is a fairly decent character, so you might be okay with it.

7th task, the special cutscene: This is the one that is shown in the picture samples. Go into the forest and get to the small house nearby. Then look for the fireplace to start the cutscene (yea, the "romantic dialogue" is super-cheesy, sorry).

Find the dot on the map, and you can unlock the secret ending (if you have the latest version).

K, gonna test play versus Yakira to see if I can find anything out.