Part I. I replaced the toilet in my lower level family room on a “temporary” basis-it's a long story but I needed a working toilet.:) The flange is cast iron and connected to a cast iron drain. The flange was still good, but a portion of the pipe, the upper edge towards the back of the toilet, appears to have rotted away, or was broken when installed. Size is maybe about two inches across and one and three quarters inch down. The flange looks like it has a pretty long nipple (? ) over the OD of the pipe and everything seems solid and dry with no other rotting. When I removed the old toilet this missing portion was filled with the ring sealer, like it was there since the house was built. I bought the house from my parents so I know its history. The original tile was still there, the toilet was never removed as far as I know, and in fact what ever was used to seal the toilet didn't look like wax but some type of plumbers putty. It was hard to remove. Were wax rings used in the mid 60's and should I be concerned about the small missing section of pipe?

Part II. The new toilet sits a bit high off the floor so I shimmed both sides so it doesn't rock. The floor is concrete and level and the flange is flush with the floor. The shims are pretty thick so even when I install the final tile flooring there will still be a gap. I test fitted both the new and old toilets without the wax ring and they both sat off the floor, though the old one originally was to the floor. The new toilet doesn't leak. I just snuged up the closet bolts but that didn't pull it down much. I used a standard size ring. Did I not use enough force in seating the toilet? I just want be sure to do it right on final install...

1st part: hey if it didn't leak before I wouldn't worry asbout it.

2nd part: I seat toilets on the wax rings by sitting on the bowls and wiggling.
It doesn't sound like your bolts are as asnug as they could go. But as you may know, you don't want to overtighten them. I have never used shims and would shy away from it.

Part1,
The toilet bowl has a "horn" that extends about three inches down past the flange so that gets you past the bad section of the close bend.
Back before there were wax rings we used plumbers putty for a seal.

Part2,
Shims are necessary when you have a uneven floor. We use sheet lead to avoid chipping the China bowl. Most hardware stores now carry plastic shims that work just as good. DO NOT use metal or wood shims. I have shimmied uneven floors up to 3/8ths of a inch. To seal the gap and give your job a professional look purchase a small tube of Dap White Tub and Tile Caulk and grout the base of the toilet.
You seat a toilet by placing a wax seal over the horn of the bowl and placing it over the closet bolts in the flange. Once placed, give it a little twist while pushing down to seat the seal. Now tighten the closet bolts. CAREFUL! Do not over tighten as the China is brittle and will crack. Tighten the closetbolts to the point where you can't move the toilet by twisting it and then stop.
Good luck, Tom