I don't really understand what you're saying in about the 1000ad/600ad gates.
I'm saying after the first visit to EoT, I went through the gate to 1000AD Medina, went through the magic cave to get back to the gate in the millenial fair to open the gate path in EoT there, and then went to the bucket instead of going to 600 AD once that path was open.
I'm actually strictly following the vanilla progression for this playthrough, so I can hit every single ending on one go.
*edit- If trying to enter the gate in the residence in Medina, I sometimes have to open the cupboard 3-4 times before the gate actually opens to transport me to the EoT.
minself -> mineself.
*edit2- BUG REPORT:https://www.youtube.com/watch?v=ZcPtUuAsYlc
I don't think you'll have any problems spotting the issue.
9 The Oath ("The Masamune!") 
Beat Lavos after the Masamune is repaired and Frog joins you. You
start out at Lucca's house, where she is fixing Robo. When she
complains about Crono sleeping in the corner, Marle defends him.
Frog goes to leave, and Marle complains she just made some tea. Frog
says he has business to attend to. During the rest of the credits
you see scenes of Frog. He defeats each of Magus' fiends, and then
goes after Magus himself. After the battle with Magus, you see Frog
standing on top of the statue above the gate to Magus' castle.
*edit3- one slight annoyance I've found in the Lavos fight, is that if the right bit is the only part of Lavos's final form left, any single target attack will default to your drone, rather than Lavos's last bit.
*edit4- BUG REPORThttps://www.youtube.com/watch?v=tlHjk5FcvE0
This one happens if you return to the Sun Palace after you get the Sun Stone in NG+.
What I think is happening is:
Since the flag for the Sun Stone being fully charged, grabbing it starts the scene that gives you the Wonder Shot and Sunglasses (including transporting you to Lucca's house). Because this is happening in an unintended area, whatever flag sets the glowing and flashing lights effects from the Sun Stone never gets turned off. You'll notice the character glowing changed when coming from the top or the bottom, which sprite glows seems to be whichever loads first, so the bottom one when coming from the bottom, and the top one when coming from the top.
This effect persists if you leave and re-enter the Sun Palace.
I'll try and check if the effect persists in future timelines once I get the Epoch with wings... if I remember, lol.
*edit5- I think your new ending from beating Lavos in the Zeal Palace is broken. (spoilered, because I discuss the new ending in detail)
I beat Lavos's shell (btw, what's the FroznFlame for? Or is it just a random Chrono Cross reference?), and it jumps to your party in the Zeal Palace throne room. When you finish walking around listening to everyone thank you for saving Zeal, and try to leave, you're taken to Chrono's new "hut" (gotta love Ayla, lol).
Once you finish exploring Chrono's new palace, you examine the book, it asks if you'd like to end your adventure, you select yes then.... You're dropped in 1999 AD, all the areas are unlocked, you've recruited Magis (despite him fading to nothing when you beat Lavos, according to Janus), and all your equipment has changed.
Then, when you use the time gate in Gobb's house, it takes you back to the EoT, and you're back in the actual game, with the winged Epoch, and the Old Man telling you to go in the bucket to face Lavos, and 12,000 BC is in it's post-destroyed state...
Oh, and there's a guy in one of the 1999 AD areas asking for... I think it was a 'lifespark' which he says only grows in toxic swamps, but for the life of me, I can't figure out where I need to look, everywhere I can think of that might count doesn't seem to be it... Where do I have to look for that?