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This article, part 2 explains the bowl installation.
Prepare the tank:
I usually prepare the tank and set it aside. You may have wondered when you read the material list why I told you to buy a set of tank bolts for a new toilet when they should come with the new toilet. The reason is because we are going to install this they way it was done in "the old days" before all the manufactures starting trying to do everything as cheaply as possible. Place a rubber washer on each of the tank bolts and put it though the hole in the tank. Then add another rubber washer, metal washer and nut to the bolt. Tighten to a good snug fit. The rubber should just compress. Do not over-tighten or you may crack the tank. There are two very important reasons why we do it this way. First it will make it much easier to install because you do not have to use the screwdriver to hold the bolt head while attaching the tank and more important is that it much better at preventing potential future leaks.
Set your toilet over the flange and use your level to determine if floor is more or less level. Anything within the bubble front to back and side to side is fine. If it is level you won't need the rubber shims you bought. If it isn't take note of the approximate location where the shims may be needed we will cover that later.
Remove the bowl and place your flange bolts into the flange. You may be using the two small slots or you may be using the adjustable slots. Whichever you are using the bolt should be turned so that the wider part of the head has the most contact with the bottom of the flange. Put on a pair of your gloves and pack the area around the head of the bolt to hold it in position or use the provided sleeve bushing. The two bolts should finish at 12" from the wall. At this point a piece of tape placed on the floor with a line drawn where the bolts are located will make the bowl setting a bit easier.
Take the bowl and place it upside down on the floor. Stick the wax ring around the horn with the plastic flange facing up. Press gently to stick it to the bowl. That flange is meant to drop into the floor flange when the toilet is turned right side up.
You are ready for the final step which can be amazingly easy if you marked the bolt locations. Gently lower the bowl onto the floor flange, place your shims under the base and gently press the bowl into place. Check with you level to verify you are still within the bubble. If you are level then test the bowl for wobble. Add any shims as necessary to stay level with no wobble. Do not pull the bowl back up unless you have another wax ring. You must not try to reuse one.
The base for the plastic bolt cover goes on the bolt, then the metal washer and finally the nut. Snug each side down hand tight and then using the smallest wrench that own tighten each side just a turn or so alternating between the two sides. Keep the level on the bowl as you do this and make sure you are inside the bubble. When finished these bolts need to be snug but it is extremely important that you not over tighten them. You can break the flange, the base of the bowl or even cause an internal crack that leaks water a little at a time for years to come. Trust me on that one. I learned it the hard way.
Most of the closet bolts sold today have beak points that make it easy to cut off any excess height. Even with that feature I like to drag a good sharp hacksaw across the break point a time two to prevent undue stress on the bowl while snapping off the extra length. I mean, heck, we are almost done. Do we want to break something now?
Snap on the plastic caps for a finished look.
Part 1 covers tools, preparation and old toilet removal.
Part 3 explains the tank installation and final steps.