Hi Steve,
You say your existing subfloor is 3/4" T&G but you don't say what it is. Is it 4x8 plywood panels, OSB or T&G planks? IMO, it is NOT necessary to replace subflooring due to stains from urine UNLESS the subflooring is badly delaminating. All you need to do is paint over those stains with Zinser shellac/primer sealer. This will block out any odor from escaping. You may wish to do two coats. Also, covering it with asphalt felt then the flooring should stopped any odor from escaping. There is also a product called "Urine Off" available at flooring distributors but I haven't tried it. As for the high spots, it is easier and better to sand them flat as opposed to raising up the surrounding areas. Get a power sander OR use a block plane or a course rasp. This will remove the overwood much faster. If after you've done your best, let the installer address any high/low spot issues. Or ask him to do it now and pay for it. It sounds fairly minor. I would take me maybe ten minutes using my edger and some 20 grit sanding discs. I'd avoid removing subflooring unless it's rotting, delaminated or in some other way faulty. The odor can be contained fairly easily.
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