A 3-foot or 4-foot prybay may give you added leverage for lifting the subfloor/underlayment panels. A 6-pound mini-sledge can be used to force the prybar end/blade under the pannels. Making relief cuts every 6-inches to a foot with a circular saw can also help by relieving some of the pressure and separate panels into smaller sections easier.

Make sure your blade depth isnt to deep ... just the thickness (or slightly less) of the layers you want to remove. Also, use adequate safety equipment (hand, eye, knee, and ear protection, etc) and follow tool manufacturers instructions and safety guidelines.

I'd take it down to the original subfloor then the tile will be even with the wood floors. I feel it's best to not compound problems.
Every floor guy down the road will thank you.