The old floor in the bathroom consisted of plywood, and a layer of vinyl.

I had torn all of that out, added a new layer of 3/8 plywood, and approx 3/8 of self leveling compound on top. I had a gallon bucket over the old drain for the toilet, and it shifted when the SLC was drying.

1) What is the best way to go about this? Should I chip away the SLC, and install the new flange(?) on the plywood floor?

2) I know they make some kind of extended version of what was there, but how do I go about figuring which size I will need?

I don't recall the model but, I have a Toto on order. I'm hoping to have all of this installed soon. The tile on the floor right now is just to see how it looks. In case anyone is wondering, I did the SLC because I also installed a warming system in the floor.