If you are a DIY person and have the technical aptitude, Liberty Gears makes a nice upgrade kit for the 3650. Comes in around $1200 when I checked a couple years ago. You can even go so far as to request custom gear ratios. I think they rate the upgrade at 600 ft/lbs, not positive. I looked into it a few years ago so I knew what to keep in my mind for when/if my 3650 goes south. Liberty presented the cheapest solution in quality parts. I believe there is a post in Tech archives of someone who actually did the 3650 rebuild/upgrade. Worth a search.
Bruce is correct though, beyond the power tolerances between the 3650 vs 6060, the 6060 is simply a better designed tranny regardless of what you put inside the 3650. You'll get your more bang for your buck out of a 6060 than you will from a built 3650.