I have a 00 Dyna and was looking into a big bore kit. I looked at SE, didn't impress me, looked at the S&S 100" sidewinder, I like it but as I looked into it more and spoke to others this is what I am doing. I am going with a Zipper 107" kit, Going the whole route, heads custome ground cam and all the other support items. This kit is capable of 150hp and well over 150lbs tq but am going to keep it at about the 120hp/tq to keep the bike reliable.
Don't forget these are just my choices but one thing I would do if I was you. Talk to the shop or shops you plan on having the work done at and see what kits or manufactures they have worked with. You don' want to just say you want an S&S kit and have them use you bike to learn on how to set it up. Go with where their experance is, you will be happier in the longrun.