Here's some of what I think: It's been pointed out Cyrus body was burnt and disappeared or what-not. That still does not rule out the fact his armor remained; maybe what little remained of Cyrus was buried. After all his spirit is nothing but an empty suit of armor.
I'm pretty sure it was indeed Frog who buried him, and of course parallel to the Garai/Radius/Isle of the Damned story in Chrono Cross, the negative/lingering sentiments of Cyrus began to transform the place into a forsaken ruin, infested with evil spirits; both Garai and Cyrus had links to the Masamune, one being killed by it, the other wielding it in life.
Strong evidence would support Cyrus' spirit wrote his own epitaph, perhaps his soul filled with regret and feeling weakness for being unable to defeat Magus, which turned him into the undead evil spirit in 1000 AD's ruins.
Also, the regret only seems to grow when the spirit of Cyrus speaks to Frog later, after recognizing him as Glenn he screams and begins swinging his sword in the air wildly, possibly further regretting that his actions also caused Glenn's transformation into a monster as well.
Moreover, speaking of why the far-removed Northern Ruins, it's possible that Frog would want to keep Cyrus' remains away from Magus/Ozzie who have the power to reanimate the slain as monsters as well. Imagine how the Guardia army would react to some sort of undead zombie spirit they could recognize as Cyrus? That would be an even bigger morale killer than Cyrus simply being dead.
