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If you mean that you have to restart an entire project, then it's not necessarily needed. You will need to create all maps from scratch though.  Depending on how far you are in your project, it's something to consider. Though to up the quality, I'd recommend starting from scratch as that way you go into the project with a fresh mind and a new perspective, and are less likely to have any issues lying in wait. Also helps getting that new perspective as MV and MV3D is two different worlds :)

"You will have access to all future updates."

You should have a page with all your purchased items. This will be located there. Once this is updated, it will be accessible to you again without having to pay any additional fee.

Yes, you can use custom tilesets. Just remember that you need to specify how each tile should work. You can define them in the "Note" field in "Database" -> Tilesets" and in the bottom right corner. You have to do this for each tileset. As for having to create a new project, no, it shouldn't be necessary. However, if you have created your project in 2D, I do recommend creating new maps with the old ones as a blueprints considering that it doesn't translate well from 2D to 3D.

Would take too long to explain it all in a single post, so just youtube "rikyu mv3d" and the top result should be a playlist going through everything you need to get started using the plugin.