Here's a good start for the nuts and bolts of it:
http://bigbf.com/bigbf_shop/mod_i-s_trunk/As far as speaker wires, I would just unplug under the right-side cover. Mine are aftermarket Electrical Connection speaker wires, I ran them along the trunk rails anyway, so it can come off as one piece. I don't know about the factory speaker wire setup, but I can only imagine it pretty much does the same thing.
For the taillight wiring, I
think there is also a plug on the right side near in front of the rear fender; but you have to double check that one.
Don't forget you need to add a Standard/Tourer taillight also.