Trim a piece of 16 ga. sheetmetal to it almost perfectly flush with the antenna hole. Some people do it differently, but I stitch weld the filler piece up until I have a full weld all the way around it. Also be sure the filler piece is sitting flush with the fender, next grind the welds down. When you're done grinding if the welds were done right then it should look like one piece and you shouldn't be able to see where the antenna ever was. Next add the filler and start blocking.
I've never shaved a 3rd brake light on a 94-98 model, but you would do it the same as the antenna, just be sure it's contoured with the cab. You will also want to take your headliner out so you won't catch it on fire.