Remounting toilet
Frankie, your plan for the toilet sounds great. Don't neglect to put additive in the epoxy-- milled fibers would be the very best but really anything like silica powder would be fine. Avoid Microlight or microballoons-- neither is dense enough. A consistency like peanut butter too recently taken from the 'fridge will be ideal.
If you're committed to using lag screws, put little mold-release agent on each one and set them in the curing epoxy mix. Allow space for the toilet flange, etc. When it's all cured, carefully back them out (use direct contact with a soldering gun if necessary) and daub them with 4200 before installing for good. You might use a bead of RTV silicone (the structural stuff) around the toilet flange, just to keep out water. Avoid the clear bathtub stuff-- it will peel out from any scrubbing with mild cleaners, just as it does at home. Water under the flange will smell and foster mold as though you meant for it to.
You might consider setting machine screws into the epoxy instead; these will grip surprisingly well and will be easily removable (if only with solder-gun heat) in future. It's a little more refined that the coarse threads of lag screws and will correspond to the epoxy filler better.
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