When my husband did my bathroom and my mother's bathroom, he used a piece of paper as a template. It came out perfect. Good luck!
I would use a hack saw blade to cut the tile. I think there are very thin blade to get in the tough spots.
How about first using a piece of paper or cloth or something that you can bend around the toilet base, and making a template with that. That way you can keep re-doing it until you've got a perfect fit, and then trace it onto the tile to cut.
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