The lowering bracket covers up the rear chain guard screw. So, before I put on the brackets, I took the chain guard off. The other modification that I had to do was get shorter fender strut bolts. The stock ones on my bikes were M8x1.25 in 40mm length. I ended up getting bolts from Lowe's that were only 30mm long and work really nicely.
Boogieman also suggested setting the rear shock preload at one notch higher than stock and it is supposed to provide the best ride quality.
I have only ridden the bike ~10 miles so far around town to see how it goes. The ride height change is noticeable. If you have aftermarket pipes that have a bracket which is mounted by the lower rear peg holder, you will probably be having a scare if you get deep into a corner. Mine are shorter and are mounted in a different place. They haven't hit yet anyway.
I'm heading out to do a longer trip today and will have a better idea of any issues then. For now, I am really happy with how the bike looks. (By the way, I am running a solo seat on an 2006 America.)