First, here's a cool toy to compare a large list of cams.
#1 204 vs 254e-- The 254e is an emissions legal cam that while adding some, it's in the "barely worth it" category. In the cam comparator listed above. Compare the 204 and 254 and take a look at the overlap number. 3* on the 254 vs 30* of the 204. Overlap is the time the exhaust and intake are open at the same time, the intake opens before the exhaust closes allowing the scavenging effect of the exhaust to help draw the intake charge in. This makes for a much more "efficient" cam and is key to making power.
Also notice the intake close ABDC number, 34 on the 204 vs 43 of the 254, closing the intake earlier allows the 204 can to build more dynamic compresion which builds bottom end torque.
#2 Matched properly to the rest of your combination a cam in the range you're talking about will have no noticeable driveability issues. This is one of the neat things about EFI, the issues with cam events screwing with the fuel delivery go away. In fact, the fuel charge can now be timed with the cam events making things work really nicely.
#3 Mods vs warranty is completely up to the dealer it seems. In most cases if the dealer installs SE parts they are covered by warranty. Discuss it with them to be sure.
#4. I run the SE204 in my 103" '11 RGU, V&H true duals, slip-ons, Ness Big Sucker and Power Vision tuner. The heads have not been off the motor. Never had it on the dyno, but from what I've seen of other's dyno charts it should be in the 105-110ft/lbs area. It runs VERY well, is well mannered and gets good mileage.
I ran an Andrews 37 in my last 2 bikes(95"), ran well, but the 204 makes more power in a more useable range than the 37.