My Opinion & FYI for others:
When you Root & don't Rom, do not uninstall any apps and you should back them all up as soon as rooted (see apps for it below)
then, only "freeze" stock apps so you can test the phone after reboot to see if there are any issues, issues may arise at anytime unexpectedly like in this case, there is no simple way to check all apps & functions. just be sure of what your freezing.
if there is an issue u just "defrost" the app and its back in the process after a reboot, if using any of the above apps its easy to see what apps u froze so u don't have too write them done & just click to defrost the frozen app
partial list of apps to "freeze" apps after rooting: titaniumbackup pro, mybackuppro, rom tool box (all great pay market apps)
if you go to xda frums there are several list of apps that you can freeze, but each persons list is different, it depends what u want with your phone
i rooted , kept it stock & "froze" several stock apps, ie nascar, sprint wallet, sprint id, other bs and my photon is much faster and battery life increased from 8 hours to 18 hours regular use!
there is plenty of memory on the photon, so you really do not need to uninstall or remove any apps
I feel just rooting the photon which is simple enough is a great improvement on its own, i am not even going to rom cuz it is fast enough, great battery life and don't have to reload everything up, i have around 120 apps on it. and yes everything is backed up several times and updated app data is auto scheduled in titanium backup
more reading over the xda forums
good luck
