Did you replace the motor mounts?
Come on now Black9!!! I'm no mechanic because I don't want to be.  
 
Here's what I've done before I determined it was internal.
First actually was the isolators; front and rear motor mounts.  I actually had to do that twice because I got a bad rear mount from the factory.  (imagine that)
Replaced The top engine mount
Replaced The swingarm bushing/bearings
Replaced The fork tube springs
Replace The neck bearing
Replaced The brake rotors (thinking I might have a warped rotor)
Replaced Tank mounting hardware/grommets/etc
Replaced Exhaust mounts
Powdered and Black-lighted the frame lookin' for cracks
Checked the transmission bolts
Now, I replaced these things each time the other thing didn't fix the problem.  I can't think of anything else to do.  One guy actually told me that because the new polymers don't absorb as much energy as the old epdm-type material that I"m going to feel more vibration than I did before.  He said that I basically have a new bike after replacing all those bearings and bushings, etc.   My thought?   He's full of it.  I've ridden that motorcycle across country at least 1/2 dozen times.   I KNOW there's something wrong.  And to tell me there isn't is just a frkn insult. 
I then went out in search of anyone who had a '98.  He let me take it for a ride.  It didn't have as many miles as mine but still, it didn't have that vibration. It was as I remembered my bike to have been.  Even though I have a new SB, I really love my wideglide.  The reality though is that it's gonna cost some $$$ to split those cases and take care of the crank.  And then you can't stop there, right?  That would be stupid not to consider re-working the cylinders, valves, cleaning up the pistons, new rings, yada yada.  I don't have the tools to do all of that and I don't know anyone who's going to do all that work for free or next to nothing.
Sell it?  It would break my heart but it's something I've considered since I don't have the $$$ to fix it and I sure hate to see sit in the back corner of the shed. 
Peace