I have a 2009 ultra that needs a 6 speed. The main shaft bearing in the bearing housing allowed the main shaft to walk. In doing so it damaged the main shaft gears, bearings dog rings etc. The forks have wear along with the shifter cam shaft assembly. Of course the main bearing is bad along with the needle bearings. Whom makes a 6 speed gear set complete without case? I found them for pre 2006 and after 2010.

 

Baker would be my first go to.

 

Here you go:

http://bakerdrivetrain.com/collectio...nt=16099842755

 

An alternative is to look around for a complete secondhand trans, to replace yours. There's one for $670 on Ebay, may be others.

 

As long as the main and counter(lay) shafts are ok, trap door is ok, you may be able to track down and replace just the broken gears. Andrews (cam people) makes all of them. I think they sell by sets too.
Then you could use a Baker or Jims 6 spd rebuilt kit that will have all the shaft needle bearings, mainshaft bearing, trap door bearings, gaskets, circlips, etc.
Those run about $215-230.
I rebuilt my 5 spd for my 05 Softail Deluxe last year. It didn't need it per se, but my issue was losing forward drive, due to a bad belt pulley(aka trans sprocket) and main drive gear, and before I knew it was those two, I had bought a rebuild kit just in case.
It's a big job. Good luck.
I have a thread about it under "basskleff" on the VTWIN forum. If you go to their site and paste the following at the end of the url:
/forums/transmission-primary/405929-mid-2000s-softails-failed-transmission-anyone.html