I feel stuck. Pulled toilet due to leak under its floor. Flange looks like abs plastic but warped like parts pushed up from tile grout under or something. It is raised a bit from floor. What kind of wax ring should I put? Can i do a thick one even though flange higher than floor? Do I level toilet with shims to be gravity level or should it be level with flange?
It doesn't seem like I can do much with the flange.

clean everything up really well. test fit the toilet with no wax. shim it until it sits nice and solid. make sure the flange is not interfering. there really is quite a bit of space under the toilet for the flange and wax
use a plain old wax ring.
so remove the toilet being careful to leave the shims. stick them down if the don't co-operate. i put the wax on the bowl, others put the wax on the flange. set the toilet, tighten the bolts and you are good to go..

It's likely warped from the upward pressure of the toilet bolts. You might be able to use some screws to help pull the flange back down to the floor.

4 to 6 Screws are a good suggestion as long as they are heavy, Brass screws. Use brass washers under the screw head. Shimming prior to setting is also a good idea and make some marks on the floor to help you place the bowl over the screws so you don't mess up the wax. You will be OK.