Xenosaga help

I'm currently in the Song of Nephilim and the 3 characters that I use are Ziggy, Kos-Mos, and Shion. Ziggy has all of his Ethers and I think Medica. Shion has Medica All, that revive/mid Ether, the Dominion Tank summon, Life Shot, and that Ether that gives a character 1 boost. Kos-Mos has Satellite, Medica All, and some other useless Ethers. I have Shion equipped with that accessory that halves all MP costs and also have her equipped with the swimsuit to boost her stats. Shion and Kos-Mos are at level 29, while Ziggy's at 30. I'm in the entrance of the second tower and it takes me 5 minutes to beat enemies and they usually take away more than 75% of my HP. What I want to know is where I can get more money(other than the gameroom) and an easier place to level up. Also, seing as how the Song of Nephilim's the second to last dungeon, am I too underleveled?

I was thinking the exact same thing when I was at that point. One thing is not to worry too much about levelling up a whole bunch - the enemies are really, really strong in this area. Stronger here than what the enemies are in the next area. If you want to level up easily, though, do this:
Through the EVS, go to the U-TIC battleship (the one you raid as Junior)
Keep heading right until you encounter the doors that required you to blow up the generators to get in to. In the room in the top-right corner, there should be a guy who doesn't attack you until you go to him called Ace Pilot. He'll start out on foot and really easy to kill, then he'll go into his AGWS, which is still not much of a challenge. He's easy to kill and gives pretty good experience and money.

Thanks for the help. 1 last problem I face is my inability to extract skills. I can't extract any more skills with any of my characters and they all have an ample amount of skill points. What's up with this?

That was a problem for me too...but they mention it in the manual. You know how accesories with extractable skills have skill levels, right? You have to extract a certain amount from each level to progress to the next. I don't know how many, but after extracting enough level 1s for one of you characters, their skill level will move up to 2, and so on.

That was a pain for me, because by the time I found out about that I was already at Proto Merkaba (area right after Song of Nephilim) and didn't have enough level 1 accesories to extract to level all my characters up.

I don't think you need to worry about being underleveled with that... wow, compared to you, I was obscenely underleveled when I tore through that dungeon and the final one. You should be fine.

Don't use Ziggy. He sucks.

Yeah...my party consists of Shion (her healing spells are too good not to have her), KOS-MOS, and chaos. Most walkthroughs I've seen recommend having Ziggy, but he's not worth it.

That was my exact party as well. At first I used Ziggy, then I realized he was too slow and wasn't powerful enough to warrant that lack of speed. Then I juggled between Junior and chaos for the third spot. I liked Junior a lot, but chaos can just go to town on those gnosis.

My Ziggy's dealing more damage with Executioner than Kos-Mos does with X Buster.

chaos: First thing's first. Don't use Ziggy unless you get his Executioner move. He is pretty much useless before that. Although, his amount of HP is better. Replace him with chaos or Rubedo. If you don't have them already, get the Double Buster and the BraveSoul. Double Buster can be attained in the KOSMOS simulator in the city area (With Shion and chaos). BraveSoul is VERY helpful when you are low on life. It does more than triple your attack power. Secondly, make sure not to use those "Attack Ethers". I was expecting so much when I had attained KOSMOS's Satellite, but it in fact does a minor amount of damage. Use the X-Buster instead.

Rubedo: Also, do what Hsu said. In the U-TIC battleship, the Ace Pilot gives you a lot of EXP points, and he is not that powerful. Other than that, train in the KOSMOS simulator, or try to avoid the enemies in the Song of Nephilim. And be prepared to fight some pretty mean bosses.