Wow man, this was super helpful. You following up with me saved a whole lot of wasted time and money on my end and I really appreciate that. There is a site (benzeen auto parts) that sells 2 year warrantied transmissions for the LS 460 for around 1200 bucks. The warranty covers parts and labor as long as you use an ASE certified technician to install it. So if it is messed up they pay for the repair costs as well. Since this car was a gift, and didn't cost me anything, I am going to give this a shot. My mechanic in houston (Noah Auto Care on Almeda) charges around $1,000 to actually do the labor. I have never used him for a lexus before but they are super nice and I have used him for my other vehicles and he has always done right by me and my mother in law.
Hopefully I am not breaking rules by giving info on parts and mechanics here, but I want to be as helpful as I can to others who may have this issue, especially in the houston area. Again Tony, I cant thank you enough.