Thanks all for the replies. took just about everything off the rear of the bike to check it out. Got the bike level, and when I put a small level on the docking gear for the tour pack, I found that it's down on the left side, which would explain the big gap on the right side between the tire and fender. But I think the motor needs to be aligned still. My manual is in the mail, so I should be able to figure this all out.
If you want to do a full powertrain alignment, you need to use the special tools. Since it's unlikely your local dealer will loan them to you, and you cannot purchase them from the company that made them for H-D (I think I still have the email where I asked and they replied no can do), the alternative is to either buy a set from the aftermarket for roughly $400 or just pay a dealer or independent who has the tools to do it for you. Besides the special tools, you need a digital inclinometer to measure vertical alignment of the front and rear brake rotors.
Basically what's involved is using the special tools to set the alignment of the swing arm pivot shaft to the frame at dead nuts with the engine mounts and stabilizers loose. Once the swingarm pivot shaft shows it's aligned, tighten the mount and lower stabilizer. This will get the engine, trans, and swing arm aligned horizontally with the frame. Then you need a digital inclinometer to check vertical alignment of the front and rear wheels. Set the front wheel straight ahead, read vertical angle of brake rotor. Check vertical angle of rear rotor, adjust upper engine stabilizer to match angle of rear rotor to front rotor. Or something like that.
If you don't have the tools or someone you can borrow them from, you will come out ahead by finding a good shop that does and just have them do it for you.
Jerry