step 1: stay away from the dealer and their screamin eagle (low) performance packages.
step 2: research, research, research, find a reputable builder that offers performance packages (headwork, cylinder bore, cam, etc)
an independent shop that has experience building engines will select a combination of components that will work well together and fit your riding style, and your end result will be a reliable, powerful engine that will cost you less and make more power than an SE kit.
if you are going to upgrade your engine, it's necessary to "do it all" in order to get good performance gains. if you just do a 95" big bore to your 88, the power will increase, but not by a whole lot. If you do a complete engine build, power gains will be drastic.
it's a good idea to google search this topic and read as much as you can. there's lots and lots of info out there, and it feels really good after you learn about this stuff, you can make informed decisions and know what you're getting and be confident that you're getting what you want.