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Marking spoilers just in case. ninja

Anyone ever try this? It's pretty cool. You can use a Game Genie code to allow the party to walk through walls. So basically you can go anywhere. There is a warp to Dezolis and Rykros right outside of the right side of of the second floor of the academy in Piata. Soo....

There's a good FAQ on GameFAQs about this. It's pretty awesome. You can use this code to keep Alys forever! ^___^
As long as you follow the guide that is. Otherwise you can have some fun but you may encounter alot of glitches and some parts of the game won't work.
I really should be in bed right now. x.x
But I'll post some of my findings first. Some of this is copy and paste from a post I made on another site.
My main goal now is to find a way to keep Seth. I figure that if I can just warp to Rykros I can bypass reaching the top of Soldiers' Temple. But I'm not sure how this is going to work out. You can bypass getting Raja and Wren if you want to. But it causes problems later on... And I'm not sure exactly what the consequences of bypassing the problems would be. Mainly, if you don't get Raja you will have issues getting Kyra. Infact I believe it is impossible to get Kyra unless you already got Raja. So if you are trying to formulate a custom party this way things may not go too well.

Basically, every character must occupy a certain slot in the party. If you get them before the previous slot or slots were filled bad things happen. The character gotten out of order will stay "sticky" to the screen. They will pretty much just be stuck to the entrance of any area you are in and will not move. They won't show up in battle. The name and stats are there but no sprite, no actions for them and you can't issue commands. Attempting a macro with a character in this state will result in some or all of the enemy attacks to have glitchy graphics. Additionally going into the menu causes the game to stall and the graphics to get a bit buggy. It usually remedies itself. But sometimes the game crashes. And the out of synch character won't show up on your menu either. It stays that way until the slot or slots ahead of that character are filled. I haven't experimented with what happens if you get two characters that occupy the same slot in one party. Apparently there are some exceptions though with characters that leave you but rejoin later.

So if you wanted to bypass Hahn and Seth instead, the game will glitch up because Seth is only stable as a fifth party member.
I know you can end up with two Runes. But you may be able to get three... I'll have to see if that works or not because you can get Rune early if you like by going through the fence at Molcum. And it doesn't seem to cause a problem.

Here's some other stuff that I found:

Speaking to NPCs that are behind closed counters yeilds various results. If you can speak to them they either say something that is already said by another NPC in that town or a blank text box. Some NPCS are more like non-solid tiles though. One even glitches up when you talk to her. Most of the behind the counter NPCs are coded like regular NPCs I guess. The actual dialog for the shops and inns is accessed by the counter tile in front of them, not the NPC itself. This I noticed when walking onto thr counter and speaking directly in front of them. When speaking to them from the back or side they chat (or attempt to) like other NPCs whose counters aren't sealed off. Perhaps the ones that act like walkable tiles were coded that way to save space?

Vahal Fort cannot be entered. Probably because the Silver Soldier job hasn't been activated yet. Wren will say tha he does not have Seed's codes. But if you walk through the wall you can reach Daughter and shut it down.
I don't know what will happen if Wren isn't in your party. The game crashes during some character specific events if the character is not present. But some still work. As for it's bearing on the job, I tried something similar with the sand worm. And after beating it I had to go to the guild and actually take the job before I could collect the reward for the worm I already defeated. And there was no second worm to be had. It was quite an odd thing to do. But it worked.

Moar later.