Not every project goes as well as planned. We would be happy to spend a few minutes answering your questions.
A toilet that leaks is bad enough…one that leaks rusty water is worse. If the toilet is leaking between the bowl and the floor, then we it sounds like the wax ring is bad and needs to be replaced. The fact that the water is rusty suggests that the flange that mates with the wax ring is rusted. I would guess that when the flange rusted, it probably broke and the toilet became loose at that point and moved, which broke the wax ring seal and caused the waste to show itself under the base of the toilet.
That's a long winded way of saying the flange needs to be repaired and then a new wax ring installed. It's a lot easier to repair a flange than replace it. Try using a reinforcement ring. These are beefy metal rings that sit right on top of the broken flange. The holes of the reinforcement ring align with the holes of the flange and so the toilet bolts will sit in exactly the same place. You can secure the ring to the subfloor with screws, or if you are on a concrete slab, you can use tapcon screws.
Once the new ring is secured, install a new wax ring and secure the toilet.
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