Ahhh I get it. Wiping is like a quick format - and flashing just pushes folders and files into their respective directories?
Anyway - I have IcedHoneyBun-v.3.6 installed, but to be honest I don't notice a single difference except the ability to have multiple browser windows and the WiFi hotspot thing... I still have Sense, all the Google stuff, all the Sprint stuff, it doesn't seem any faster... I don't see any way to uninstall the Sprint stuff manually (you said that there was a file manager to do that?) and I don't see any way to store apps2sd.
What the heck? Did I mess something up or do something wrong? The one hiccup I had was that when I went to wipe the dalvik or whatever the phone told me to do it through root - and I didn't; I just continued. Does that matter?
UPDATE: I guess it still wiped the dalvik -
Error : Run 'wipe dalvik' via adb! - Android @ MoDaCo