The amp wont fit under the left side cover. It doesnt take much space in the trunk... its 2x7 ish... about the size of two large boxes of matches end to end
I followed the directions from this post... you must open the photobucket pictures to see the instructions... you need a dremel and some small cutoff wheels and I also used a grinder. The little grinder wheels like to BREAK.... WEAR GLASSES... a 20 pack of them at Menards was $3....
http://www.valkyrieforum.com/bbs/index.php?topic=33355.0The DB501s almost fit perfect in the rear without modification. I had to flatten the rounded edge facing the front of the bike by maybe 3/16" and the fit perfect. I flattened them on my bench grinder.
You have to cutoff the flanges on the original fronts with the dremel wheels but it only took maybe 10 minutes each to do..... and about 10 of those little wheels....
To answer the wiring question as a rule I will never cut a harness.... however I did cut the one going to the rear speakers as its not part of the main harness and easy to replace.
I probably did an unconventional install. Basically I pulled the gas tank (changed the filter while under there) and ran 2 sets of 4 wire speaker wire to the front. Since I wont cut the main harness and wanted to retain fader control I unplugged the speakers up front and used them for the high level inputs. I connected the other two to the new speakers for the feed.
I ran 2 more 4 wire speaker wires to under the right cover. I came back about 2 inches from where the original rear speakers plug in and cut them. I connected one set of right and left to the wires closest to the plug for my high level inputs on the amp. I reused the remaining wires to the speakers and connected them to my other two sets of wires to avoid rewiring the rears.
While I had the speakers out I also took a picture of the original wires as it makes it easier to keep track of polarity of the speakers and the original speaker wire colors.
Remember the larger spade on the speakers are POSITIVE and the smaller is NEGATIVE. The new wires I used from a 100ft wall speaker roll from Lowes has four speaker wires inside the protective cover.... Red, black, green, white. I bought that one because it simplified wire routing and the wire sleeve is black.
I simply kept both right speakers with red/black, and the left side as green/white. WRITE YOUR POLARITY down... red = positive, black = negative, green = positive, white = negative or however you'd like.... helps when you are wiring to remember and keep right/left front/rear straight when your wife comes out and burns your ears off with things that are more important to her than you.....

I'm sure theres an easier way to do it but thats how I did it.... it works great and sounds great.
I ran my 10 guage pos/neg power wires directly to the battery. I used a very thin green wire for my remote and inserted the bare end into the small fuse box, found a switched fuse, pulled it, inserted the thin wire, then reinserted the fuse. Its just a remote trigger wire ans won't hurt anything. The amp has its own fuse on its harness.
I bought the red, black, and green amp wires individually and put one end in the vice and the other end in the drill and twisted them together.... then put them in flex loom... electrical tape the ends so they dont come unravel....
Sorry this was so long.... lol