Radius found the Masamune on Zenan Mainland, not Divine Dragon Falls. This is confirmed in the Ultimania Guide and heavily implied by the game (Viper was promoted to the rank of General on Zenan Mainland, and he and Radius, Garai and Zappa "tore up the battlefield" in 1,005 A.D.).
I don't know. Inside the cave at Divine Dragon Falls, it looked all tiwsted & evil. The evil of the Masamune probably altered the area, in similar fashion to Ilse of the Damn and the gates to the Dead Sea. It may not have been there long, but Radius had to find it there.
2) Not so sure that she'd come on her own. The sword did a lot after the events of Chrono Trigger, and she never seemed to notice. Defeating Dario seems to have triggered it.
That's why I think Doreen just suddenly shown up and sounded piss at them. She must of knew about all the evil they done but just haven't found Masa & Mune until Dario used it. Cross has shown that the Chrono world is much bigger than what was seen in Trigger. She must have been searching the mainland for years, and started looking in El Nido around the point of Cross' events.
The Masamune was stolen from Guardia after Lynx provided Porre with new technology. All the killing and and massacre it was used for seemed to have turned it evil.
Wrong. Lynx didn't even exist in 1,005 A.D. yet. Porre were influenced by an help "from outside of the normal flow of time", but it wasn't Lynx.
Porre/Zenan started to migrate to El Nido in around 900 A.D., right? Either they found Chronopolis or just bit & piece of their technology in the area, and that started their militry uprise. Someone else, probably no one important, just found the Masamune around the same time (or at least after Frog's death) and used it in the attack on Guardia.