Thanks for all the input guys!
To answer a few questions:
I rebuilt the forks last weekend with fresh springs, seals, and oil. I put in equal amounts of oil and haven't seen any leaks. The freeway wiggle was the same before and after the fork job.
All nuts and bolts are secure, I've checked everything a million times since completing the bike. The shocks look really good and seem to function well enough.
Like I said, I originally had the tire pressure at the recommended Honda level. 28psi? But had a fair amount of wheel bounce around 30mph. People on here told me Honda's recommendation was only intended for tires of the 70's and doesn't apply to modern tires, and I should do what the tire manufacturer suggests. I found this page and did mine 32 front, 36 rear. The 30mph bounce went away.
http://www.avonmoto.com/tech/tire-pressure-guidelinesMy front tire is 100/90-19. My rear tire is 110/90v18. I did a lot of research before ordering and read this was the proper size for the 550, but the front ended up being wider than the Cheng Shin that it had. Did I order the wrong tire?
When I installed the rear wheel it seemed to me the only alignment method was by using those two adjusters on each side of the very end of the swingarm. I just set them so they were both at the same mark and the chain was properly tensioned.
Is there a better, or correct way to align the rear tire that I stupidly overlooked? It seemed rather primitive to me at the time, but saw no other way. I would research right now but the internet's down and I'm doing all this from my phone..