I had a shop do a 6 speed conversion a few years ago on my 2001 softail standard,my motors putting out 105hp and never had an issue with the trans,ive put about 18,000 miles on it some hard miles some easy.my issue/question is it always has whined in every gear but 5th,the shop swears its normal and he only uses baker kits.the question part is can a 6 speed kit manufacturer be identified by either looking at the trap door assembly or any other markings without pulling the whole trans out? I like the trans doesn't skip a beat but im pretty much done with the whine.they reused my original case and theres no markings on the exterior of the trap door .

 

Sounds like you got an overdrive 6 speed for the bike.. They won't whine in 5th since 5th is direct drive.. The whine is likely from the gear pitch.. About the only things you can do are try thicker oil.. 85W-140 in the tranny and buy a set of ear plugs.

As far as identification goes. I suspect that you don't have a baker..

http://bakerdrivetrain.com/od6/attachment/od6-contents

It has a new endplate and the gearset for sure wont work with the stock plate.. If you look at the pic one gear pair in inside the plate... For sure Baker puts something on the plate..

 

If you had the work done you should have paperwork to confirm what they charged you for. All early 6-speeds were overdrive, as bwoltz describes, they don't make a noise in fifth because there are no gears directly involved in transmitting drive in that gear. AFAIK most if not all 6-speed gearsets come with a new trans cover/bearing housing, so I'm surprised you have nothing visible to tell you what you have.

 

If it is a Baker it will say Baker on the bearing door. Even our OD6 is noisy in 4th and 6th it is inherent but no noisier then 4th in a stock 5 speed. Try some Redline in it 75w250 it won't eliminate the noise but it should lesson it.

 

You got burned!!!

 

Yea....SIX years ago!!