Tough question. The trade value of a F350 with or without the egr delete etc is next to nothing. Once they hear 6.0 the price drops like crazy. If you like the truck do the mods.
I went and looked at an 08 Dodge. Sticker price was 26,998. They were going to give me 6,500 for my 03. Once they added up all the numbers I was quoted 25,xxx difference. My engine was replaced at 75,000 kms for a none typical 6.0 issue. My truck had less than 4,000 kms more than the Dodge. 71,00 less kms on my engine.
I do all my own work which saves me a bundle. One my drive home from the dealer I had to wonder why I even considered it. Apples to apples not much difference
I guess I'd keep the truck do the stuff and carry on.