Did you make a backup before modding? If so, just flash the backup and you'll have the apps back. You should ALWAYS backup before changing anything on your phone.
If not, the only way to get the stock apps back is to find them in the market, or if they aren't there, get the original SBF file (the stock software for the phone) and flash it. To my knowledge, the SBF for the D4 isn't out yet.