I'm remodeling my bathroom. I tore up an old mud job floor leaving the closet flange /toilet flange at a height of 1.375" to 1.5". I will be adding 3/4" subfloor with 1/4" tile. This should leave me a flange height of .375" above my finished floor, counting my mortar. Will a closet flange with a height of .375" to .50" above my tile floor be to high?

The flange is connected to a lead 90 degree pipe that connects to a cast iron drain pipe.

Yes, too high. A flange does have range but it can be top of flange flush with floor or bottom of flange flush with floor. I would suggest you add 1/2" cement board, Hardibacker or wonderboard to you sub screwed and glued

... or remove the ring, cut off the pipe and reinstall ring

I currently have the contractor .5" sub-floor that I never pulled up off the joists. I planned on adding .5" sub-floor with .25" Hardi-Backer glued and screwed giving me the .75" sub-floor adding to what is there now. My Tile would give me another .25" allowing me to make up 1" of height. If I added another .25" on top of that would put my floor at a .625" higher than my hallway where it meets. Also making my sub-floor a total of 1.5" before tile which is probably to high.

I was hoping that a flange height of .375" was OK allowing me not to have to cut the flange. Not sure how I would connect the flange to a Lead Pipe.

For what it is worth, Beto...

If you have a lead pipe there I would tell you that NOW is the time to replace all the lead pipe in the floor... not 1 or 2 years down the road after all this work is done and the work has to be done from below... ;)

I would also remind you to check the installation instructions for installing hardibacker as hardibacker requires that you set the cement board in a bed of thinset mortar that has been notch troweled to 1/4" thickness over the subfloor.

Questions? Let us know, OK?

Mark