Motorcycle Repair: 1996 FXDWG Engine Vibrations, vacuum leaks, vibration problem

Question
Hi Mike -
I've done some reading here, and elsewhere, and I have a bad engine vibration problem on my mildly modified '96 FXDWG. It has 101k miles.

History: at around 15k miles, I upped the performance with Andrews EV27 cam, Mikuni HSR42, Dyna2000 ignition module, single fire coil, SE air cleaner, V&H Straight Shot pipes with baffles, nothing too radical. At about 50k miles I had the cylinders refreshed, SE 10:1 pistons, valve job. The bike has no intake, exhaust, or vacuum leaks, and the carb is in good tune.

The bike has been running great all these years, until about 8k miles ago, give or take. I noticed a vibration under load and at certain RPMs. No tach, so I can't say for sure where, but it's tolerable at 20mph in 1st, 30mph in 2nd, 40mph in 3rd. Vary the speed up or down a few mph and it's very uncomfortable. While in neutral and parked, revving and holding the engine at off idle rpms the vibrations are very apparent... feels harmonic to me, but never goes away. I can slowly increase the engine speed and find the point where the vibes are out of control. As one other poster commented, a paint shaker comes to mind.

I recently had the bike to a shop for new motor mounts, isolator, primary chain, carb tune, starter rebuild, and general once over. She starts well, idles nice (though a little more jumpy than I think she should be), has good power off the line and at speed. The dyna2000 is configured on curve 1, voes normal, and the voes is connected. I did a compression test and have 151psi front, 149psi rear, all seems good. Plugs look good.

I'm at a loss as to what to check next. The bike was down in 2007, left side at about 40mph. Damage was done to the primary cover, scrapes only, and the front end, but everything went back together fine, no frame damage or cracked primary. The vibration problem started prior to this incident, tho wasn't as bad. Recently it's much, much worse. I know this is not wheel bearings, tires, or "in motion" related items. I've done the test, bike is smooth when coasting.

I've read here about possible crank being out of balance. Tho this makes sense, I can't understand how this occurrs. If the bike ran for a period of time while laying on it's side, could some sort of internal damage have been done? I don't recall if it stalled out after crashing or if someone had to turn it off. I'd expect it would have stalled out on it's own.

While poking around, I noticed my Dyna2000 case had some stress cracks on it. It has been on the bike for 12 years and this is the first I've looked at it since installing it. I have read elsewhere of someone who had similar problem and replaced the module, problem solved. I'd hate to spend $300+ on a module and still have the problem. I doubt electrical items are returnable. My original dual fire module is long gone, no spare to test with.

Thanks for taking the time to read my lengthy post. I'm at a loss and don't want to get into thousands of dollars of "try this, try that" stuff without some basis for exploration. I realize the bike has a lot of miles, but I'm not willing to part with her, ever. I need to sort this out as riding season is upon us and I have miles to put on!

Best,
Jeff

Answer
With that many miles I would suppect that the rod bearings are worn and lose, which would cause the vibration. The other thing it could be would be the left main bearing is worn. The only way to be sure is to tear the motor down and inspect them.
Good luck and happy riding
Mike