Try Doug Lewis at FPS near Atlanta. He used to beef up Gen 3 ATXs, using the Ford Reman as the core. Not necessarily cheap, but they held up as well as could be expected.
Doug's shop is a natural first stop. You could go through ShoSource's vendor and get the road ripper series. There was another company that I was looking into that had been recommended to me that specialized in race applications of these transmissions. I'll have to find that one again. In almost every case expect to pay about $3K and you install it. More if someone else installs it.
For SHO Source in CA, the shop can rebuild a stronger Gen 3 SHO trans for around 3 200$ (even if they are more focused on Gen 1 and 2 SHO). It's nearer from your home. https://shosource.com/products/ols/products/rebuilt-sho-ax4n-96-99