After you free the Guru, you are one step closer to stopping Lavos.
Prepare for Lavos
Talk to Melchior to get the Ruby Knife. Then rest in the inn if you need to, save at the save point at the bottom of Algetty.
I find that the group is now at a good level to fight Spekkio again, in his new Goblin form. Remember to only use magic. Crono, Marle, and Lucca should be good against him. Try equipping your Red Mail, Red Vest, and Ruby Vest (or Taban Suit), as well as R'bow Helms on everyone. Try the Wall Ring on somebody too.
Back in 12,000 B.C., (my preferred party is Crono, Ayla, and Robo) head for the Skyway. Your goal is Kajar, the Nu has new stuff for you as long as you say that's not Schala's pendant (if you screw up just go back outside then in again). Then go to Zeal Palace.
Go through the door that leads to the queen's room. Save and go in. Go up to fight Dalton.
He's really easy: he just keeps using Iron Orb on you, which can't kill you. Have Crono and Ayla work on him with Volt Bite, and have Robo heal periodically so your HP is somewhere above 150. He has one attack that he uses before he dies, and you don't want it to kill you.