I have a 94 FXDL that was given to me and it had a cracked inner primary and transmission casing also cracked. I replaced both transmission and inner primary and it runs great except when I hit the rear brake major vibration in the pedal and rear shakes. If you shut the bike off and coast no vibration when braking. Also with the clutch applied you get no vibration. Any ideas what could be causing this?

 

Most likely the rear disc is warped

 

Since it seems to do OK on braking while coasting I would suspect when you assembled the rear end after replacing the parts you got something wrong with the wheel bearings or swing arm bearings.. It might be something as simple as belt alignment tho or a combo of..

 

I would check the brake rotor first. If the rear caliper is Locking Up It could get the rotor hot and warp it.

 

I'd bet money your front motor mount is junk. I just went thru these same exact symptoms with my '16 Wide Glide. If you go over to the Dyna forum, and go a few pages back you'll find a couple of threads about front mounts AND also a T.S.B. from Harley-Davidson showing how to check it.

 

Easy fix grinding down a relief into the pedal worked perfectly took me maybe 30 minutes from start to finish!

 

agreed rotor would cause issue running or not as long as rotors are hot. cold rotors vibrate less .my 2017 low rider 2k miles was doing a lot of weird crap with the junk motor mount from the factory. took it out looked fine not compressed but that bike just didn't like that bastard. sad at 2k miles its such junk. bad design aluminum bolt holes and bolts that are too short.