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One thing to keep in mind when installing or aligning the front motor mount, make sure the rubber mounts metal spacer is properly aligned side to side on the motor mount and then you put the bolt in the middle position front to back. What you want to end up with is that the long bolt doesn't touch any part of the rubber mounts internal metal spacer. If it does then it will transmit vibrations to the frame. That metal spacer protrudes above the rubber and that is actually what comes into contact with the motor mount, so if the bolt is touching any of this metal it will transmit vibrations. I've run into this issue with my bike and installing that bolt in the center of the spacer so it doesn't contact any metal gets rid of most of the annoying vibrations. I'm using the stock motor mount so can't comment on any after market stuff. Also going with a larger bolt to take away the space between the rubber mounts spacer will actually make vibrations worse. Motor mounts are designed to allow some movement, hence the narrower bolt.
I would be careful of shimming. On the frames, where the motor mount lifts away from it when you loosen the bolt, it probably works fine but on the frames where the motor mount sits down on the metal spacer and nothing really moves when you remove the bolt, it likely wouldn't work well. When you fill the dead air space between the bottom of the front motor mount the top of the rubber mount you are limiting the movement of the motor mount which would transmit more vibrations. I had installed a washer on mine, but after I thought about it I took it out as I couldn't see how it would make anything better. I'd be interested in hearing about those that had installed the spacer above the motor mount and how they made out.
Depending on on the year that the crank was installed you may have an SnS cranks that isn't so hot.. OP's, being a 2001 Dyna, may have an early SnS crank that has have been known to shift. I had 2, 4 5/8 cranks shift. One in a 116, that was rebuilt by dark horse after 22000 miles. It later broke the rear rod 20000 miles later..
Another was in a 131 and it lasted only about 12000 miles and got replaced with a newer SnS Crank.
Early SnS cranks were known to flex as they used a 1 1/2 inch crank pin, cast flywheels (?) , same as evos but pressed together not tapered pin. They were known as 5 piece cranks.. The later ones went to 3 piece with 1.671" crank pin (same as stock TC pin diameter) and forged flywheels, sprocket and pinion shafts.
Going from 4 inch stroke on a early dyna to 4 1/2 is going to vibrate more.. The 06 up frames had weight added to them which I suspect was to help with the vibes when the 96" 4 3/8 stroke motors were introduced. Don''t know if the issue is crank runout or simply the motor mounts but it might be worth a check. If the motor has an early SnS cranks. I'd thing about replacing as they have been known to have issues.
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