It's a common DIY misconception that the top of the flange should be level with the finished floor. This is not surprising because some videos clearly show this. The proper method (and what your toilet is designed for) is for the flange to sit on top of the finished floor. That means that the bottom of the flange is on the finished floor and the top of the flange is above the finished floor. You then drop a wax ring on the flange, mount the toilet, and voila.
So...doesn't sound like your flange is "high", unless the bottom of it is above the finished floor.
If it's a little unlevel, welcome to the real world. Dry fit the toilet. Shim the toilet so it's level and doesn't rock, pick it up, drop a wax ring on your flange, put the toilet back on the shims, bolt it down and unless I am not visualizing a problem that you mentioned, I think you're done.