The Keep is actually a lot less complicated than it might seem. Before you even enter here, I suggest making sure you have either lots of Piercing Crystals or Dispel Barrier Lv.2, since you're going to need it at least a couple times. Having all your Level 3 spells wouldn't hurt either, if you have magic users in your party.
There are lots of Vahnatai through this level, in many of the hallways and rooms, as well as a few Golems scattered around, and a couple Alien Beasts. They aren't marked on the map, just be prepared for fighting at most times.
When you first enter you'll find that the entrance is guarded by a variety of Vahnatai, and blocked by some Force Barriers. Use distance attacks on as many of the Vahnatai as you can read while getting through the barriers.
Once into the keep itself take note of the entry directly to the east, but don't go through it. This is the entrance to Rentar's throne room, but you don't want to start any fights with her until you have all the beams redirected.
I suggest completely clearing the other areas of the first level before advancing to the second level. Use the maps to see the locations of the ladders leading down.
Pay particular attention to point 3 on the map. You have to use the control panel to open the portcullis blocking access to the ladder.
There's a variety of fairly useful items scattered around the keep, in rooms, and dropped by the Vahnatai you kill, including a fair number of potions, some weapons, which you shouldn't need since you should have better by now, and a variety of potion-making herbs.
Look now at the secret passage marked by 11 on the map. This secret passage has a few force barriers blocking two doors. The northern door leads to a few potions, but it's the southern door that's the important one. This leads to an empty room with two runes on the floor.
Remember the message you got back in Footracer Province about when you near the end, pants on the west rune and step on the east rune? This is the place. They have to be normal pants for some reason, special pants, such as Iridium Pants don't work.
Once you step on the rune you'll be transported to the generic dungeon. I thought about doing a walkthrough for that, but decided to opt out, since it would kind of spoil the surprise. You don't get any wonderful items if you do it, but it's definitely worth a few giggles. If you decide to do the Generic Dungeon make sure to talk to the innkeeper when you get there. A little commentary by Jeff...Vogel perhaps?
Once you've completed the upper level make your way to the northwestern of the four ladders leading down. Each of these ladders will take you to a seperate section of Level 2. This one happens to be guarded by Alien Slimes and Dark Wyrms. It contains two of the ten control panels. Remember to push each button once and only once.
Now make your way back up the first level and over to the northeastern ladder. This section is guarded by Efreets and Nagas, and contains three panels.
Over to the southeast corner now, and down to the section guarded by Rakshasi. These things are still a pain, since you still can't do magical damage and while you're trying to kill them they're summoning like crazy. There's three control panels in this section.
The last section, in the southwest is guarded by some Vahnatai Undead, including an Undead Researcher, who is very hard to kill. This section contains the last two panels.
Now it's time for the final showdown. Make your way back to the entrance to the keep and go through the door to the east. Make your way towards the control panel, which is guarded by Rentar-Ihrno and a few of her minions. Kill the minions but leave Rentar alone...it's almost impossible to kill her, and I've heard from those who somehow succeeded that it's not worth the couple hours it takes. If you have Erika's Amulet she'll make an appearance around now and battle Rentar-Ihrno, drawing her attention away from you.
Make your way to the control panel near Rentar. When the control screen pops up Rentar-Ihrno will kill Erika. Press the Load Slime Compounds Button, then the Refocus Beams button, and finally the Begin Process button. Whatever you do don't press the Emergency Beam Cease Button or you'll have to go redirect the beams on the lower level all over again.
Unfortunately, this is the end. It's kind of a sucky ending, after all that happened, I know, but that's it, and I hope you enjoyed the game.