Hi and welcome to the forum!
This is the first time that I have heard of bottom end problems on a TW! Top end problems? Yes, lots of those.
I don't know about the availability of new or remanufactured bottom ends, but used ones are certainly abundant. I have at least 3 complete ones sitting on a shelf and almost all of the parts from a few more. Have you confirmed that it is the bottom end that is bad?
Tell us if you have the tools and skills to tackle a rebuild by yourself (with our help, of course), and where you are located. There may be someone nearby who could help you out.
p.s. The good news is that the bottom ends of all TW's are the same, so you have 32 different model years to pick from (but hang on to your kickstarter, you'll want it if you use one from a 2001+ model year)