I would go with the 103" kit. I just purchased a 2010 FLHTCU last Saturday because I wanted something more comfortable for the wife and I to go out on besides my night train (plus they took close to 5k off the sticker price so they could make room for the 2011's).
I have a stage IV kit on my 2007 night train and that bike is fast enough for me. For the 2010, talking to dealer now - said the 103" kit would be $1500 installed. Since I am having the stage I kit done (pipes and air cleaner), I would save roughly $300 dollars on dyno tuning by doing all at once.
I have until the bike goes in on Tuesday to decice if I want to do the 103" kit. Being a full dressed bagger, bike runs hot to begin with. I am going to install oil cooler and change to synthetic oil at 1K service. Dont know if I will even touch the motor since I have the night train already.
As for your question, I talked to the mechanic who did the work on my night train and he told me to stick with the 96" motor, change the pipes and air cleaner and just ride the thing. Sure the 103" would have more torque and power, however, it would have more heat as well. He told me if I was dead set on doing work to the engine, then go with the stage II 103" kit with S.E. cams. He told me if I start going larger displacement, due to size and weight of bike - and fact that I will be doing two up riding - I am just asking for issues down the road.
Hope this helps.