I agree. And it's a pretty easy albeit a dirty job to fix. Don't forget to turn the water off and then drain it. For all intents and purposes, you have one shot at positioning the toilet on the wax ring to let it mold around the base and form a water tight seal. DON'T MOVE IT AROUND. Then just bolt it back in and caulk. I recommend caulk along the bottom where the toilet meets the floor after you've reinstalled. Otherwise, centipedes like moisture and they will harbor under there.

Liquid Wrench might work better than WD-40. I've had to go so far as to cut on the nut with a hack saw/file/dremel tool until I could cut it off with a pair of dikes. At least you have the tank off of the stool so you have better access than when it's installed.

Based upon your description I suspect the part you are describing as a kit with a rubber ring is in fact a "Flange Extension bushing" (sometimes called a flange buildup bushing) and you have it installed incorrectly. A flange extension bushing is a flat PVC plate made in exactly the same size and shape as the top plate on a closet flange and it has a rubber gasket surface on the underside. Begin by examining the original flange. There should be four screws through the flange than hold it down to the subfloor. Remove those screws, then lay the new buildup flange on top of the existing closet flange with the rubber gasket side down. The gasket is intended to seal the new buildup flange to the top of the existing closet flange (Although it is technically not required, I usually apply some clear silicone sealant to the rubber gasket material before installation.) Now align all the holes and slots on the new buildup flange so they match the holes and slots of the original closet flange. You can now install the four screws. passing through both the buildup flange and the original flange then into the subfloor to secure the closet flange in place. The top surface of the buildup flange should be about 1/8 to 1/4" higher than the finished floor. Now install the two closet bolts on from the underside of the original flange, up through the slot of the buildup flange and on up were they will secure the closet bowl. (You may need to get longer closet bolts which are available at any hardware store.) Now install a new wax ring and set the bowl in the conventional manner.

If there's water on the floor and there is no drip to be seen, it's most likely the wax ring. This is a simple fix, especially for someone with your experience. If you need details, there are many YouTube videos showing how to replace the wax ring.