Cast iron can be a problem for DIYers. The very best thing to do is to hire a plumber to properly install a flange at the correct height. If you determine to DIY, then shortening the pipe and installing a flange with a no-hub connector would be the best option to professional help. You do not use a "rubber boot". These are intended for buried connections only. I'm not sure by your description if you are aware that the flange is supposed to set on top of the finished floor. In addition to the drain connection, it is anchored with screws through the finished floor and into the sub floor. I'd recommend you get the floor completely laid leaving the pipe extending through the floor then call the plumber to do the flange work. That would be the best way.