You could probably find a stock ROM that matches your version in the development forum that you could get the apps from. It does not matter if you get a rooted version of the ROM. You just want to get the odexed stock ROM that you can get the apx and odex files to replace the ones that you have removed.
You can remove the system files if you are sure that you will never need them again. Freezing them is a way of preventing them from running without actually removing them... useful for testing to see if removing the program causes any unforeseen problems.
If you have removed a file and now have changed your mind about not wanting it (i.e. Now that it is football season you find that you really do want Sprint NFL back) it is also possible to get it back without reflashing. You can extract the apk and odex (if any) out of the stock ROM and place them back in system\app. I have done this with Root Explorer. Make sure that you set the permissions back (to 644) after copying the files.
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