@Yankee Dog
I understand the 90° level on the rotor but what do you use to make sure the frame is perpendicular 90° to the ground?? Thanks..

 

Gents, thanks for the input. t150vej yes it does vibrate when standing still in neutral and I did loosen the belt before so Ive just re-tightened it (possibly a bit tighter than should be but just testing it) to see if this makes a difference (Im leaving for work in 5 minutes). When get to work ill let you all know if this has helped.
Yankee Dog thanks for confirming about having the bike on the ground when i have all motor mount bolts loose to find "neutral" - i had mine on the lift so hopefully when i do this again it will also be better centered.
Racepress...thanks for the insight into the top mounting bolt and the learning that its a "Heim adjustment link" I shall use that to impress my friends One question, you talk about setting the engine vertical with this.... "Once Drivetrain is Straight in chassis...I align the rear wheel to the Belt (or Chain)". Can you run us through how you find the 90 degrees? I will have to review the tracking on the rear belt drive later but it makes perfect sense and im pretty sure mine has never been "centered".
Hotrod, nice question because if this is wrong then everything else is out of whack!

OK rode in to work with a retightened belt and yes I think it was a little better...I'll be loosening it a quarter turn just to set it right BUT I think I need to start realigning from the very beginning again starting the getting the Drivetrain straight in the chassis - if I can.

Also Had a look at the rear pulley to see if it was tracking left or right but mine has a lip on either side which doesnt really let the belt mover so i dont think I can check it with this system or are we talking millimetre's of movement?.

 

I watched a bunch of youtube videos on checking and trueing/aligning motorcycle frames, bent frames, etc. Came to the conclusion that a bubble level would do the job for me. I remove my seat and place the level on the portion of the frame that is normally under the seat. It's a nice flat part of the frame just behind the tank. I did confirm in the past that particular area is a true 90 to the down tubes of the frame using string, plumb bob, steel ruler, and again a few levels. Only want to do that once...

I use my bike jack under the frame making sure it is touching the frame only to get the bike standing upright but I try not to take any load off the suspension. Sometimes I will use my front wheel chock to do the same thing with no difference noted (I use straps from the rafters to the handlebars incase bike wants to fall over). Inclinometer on the front and rear rotor and bubble level on that spot under the seat.

I do wonder about how those new fangled laser thingys would aid in this alignment procedure, but might just drive me crazy also. The way I do it seems to work and once you get it right, you really don't need to mess with it unless you disturb things like mounts, inner primary, etc. Just a rear wheel removal is a simple thing and won't affect engine alignment on a FXD,

Anyways a couple wood door shims if I need to adjust between the frame and the jack so the frame at the seat is perfectly level according to the bubble. I keep the jiffy stand down and block it for some stability and additional shimming under the jiffy if I need to or instead of or additional shimming at the frame.

There are tons of videos on measuring/determining frames and bent frame alignment so I won't post any of the many links to those. However:

This video is good at showing how "actual degrees" relates to a bubble level when the bubble is at certain positions on the level (the bike frame is stripped and sideways):

 

Forgot to add some ramblings on the subject and I don’t wanna sound like a broken record, however, the FXD is an interesting beast. I don’t know if other models are set up this way.

The rear wheel bolts to the swing arm and the swing arm bolts to the transmission. The transmission is connected to the engine by the three bolts that pass through the inner primary and the two larger vertical bolts up behind the rear cylinder.

So all those components are connected and can mismatch from the rest of the frame. That’s why engine alignment is important. It’s also why I stress when installing an inner primary, the procedure in the factory manual needs to be followed. Any uneven alignment or torque will skew the settings or crack the inner primary.

I also have a suspicion that is one of the reasons the lip at the engine stater O-ring can break as well. Too much tension or uneven tension on that lip or a loose innner primary to engine mounting bolts/connection.

 

When you say 2k rpm's do you literally mean at 2000. Or are you describing 2500. If you're riding it at 2000 rpm's that way to low.

 

I've just found this on the forum and I think it shows how you can get the frame 90 degree to the ground and after that use the top mount to get your rear wheel brake disc also to 90 degrees if it is out - this is basically what Yankee dog said for Hotrod. What I'm not sure about is how do you then align the front and back motor mounts as you're supposed to remove the top motor mount and if this is under any kind of tension (unless you've loosened up both front and back motor mounts) it will potentially misalign again.

Would I be correct in saying then that perhaps one way to align everything is the following:
- stand the bike up to 90 but with wheels on the ground (using jacks and shims)
- undo the bolt on the top engine mount and take it out of its hole,
- loosen all the bolts on the front and back motor mount,
- set up an inclinometer/bubble level on the front brake disk to 90
- set up an inclinometer/bubble level on the frame under the seat
- set up an inclinometer/bubble level on the rear disc brake
- adjust engine "by hand" moving the top left or right until all readings are at 90.
- with wheels still on the ground run the bike for 30 seconds to settle it into place.
- re check all the levels
- tighten front and back motor mounts up (using shims if needed)
- finally, adjust the arm of the top mount to fit into its hole without any tension.

Then you should have a pretty well adjusted engine, trans, wheels etc.
All this assuming your rear axle/wheel is corrected, your belt is as tight as recommended.

Does this make sense?

 

@Yankee Dog
That's pretty much exactly how I do it. I remove the seat and I have two big anchors in each wall of my garage.. I use my tie down straps to stabilize the bike to get it level with a bubble level on the frame and then start lining everything up. Once I have the frame straight I go to the face of the throttle body Believe it or not and I check that and then make my adjustments to my heimjoint up top to push or pull the motor to get that perpendicular to the frame... It works very well.. Then I'll adjust my rear wheel with only a quarter inch of belt tension at 10 lb with the gauge. I have found that setting belt to 3/4 in is way too loose and if your rear wheel is out of alignment the belt will climb up on the side of the pulley and snap it I've done it twice...
The final test I do to see how well the belt and the alignment is tracking is down the road between 60 and 80 mph, twisty roads because if the rear wheel is not a line properly you will feel the bike tend to lift while cornering going left or right If you get no lift in the bike on left hand curves or right hand curves (more noticable going over bumps) you know the rear wheel is inline properly to everything else.. I can corner at 120 mph mind you they're not small corners they're big sweeping four Lane highway type roads..

 

The Belt has room..visual room on each side of the "lips"..
I am gonna leave My FXR procedures Out of this Dyna Discussion...They are Not the Same.

 

Unfortunately on both ends of my commute I have a couple of miles of built up areas and speed bumps so all of this is at about 30mph and 2k rpm, literally the worst speed for my vibration....I try and adjust up or down bit but only to avoid the vibrating.

 

You're lugging the engine at 2k rpm. Try riding in a lower gear. Somewhere around 3k~3.5k the engine should go glass smooth in the chassis. Learn to ride it in that zone you and the bike will be happier.