Maybe if you look at listed prices (sticker price) you are correct but with the discounts, rebates and dealing the $6,000 price comes down a lot especially when you can purchase the vehicle on the lot. I found out it was very hard to get a fully equipment regular cab WT/LS model in April where right now I could get an LT for the same price or a little less with more options. Usually a double cab has a $3,000 - $3,500 difference in sticker price over a regular cab but with the better rebates/discounts etc. on double cabs - the price is a lot less. GM and other dealerships are having a very hard time selling off their 2016 right now. This has been in the news. It all depends when you purchased the truck and how you worked out the price.
Installing these options has no increase trade in value and there is no warranty coverage because it is going to be looked as a WT/LS trim level truck. I know right now I could get an LT for far less than $6,000 sticker price and maybe some what a little over $2,000 but I also would get some more additional options other that is mentioned here as well. There would be also a savings on your additional labor time (which is not counted) and possible issues or problems with your warranty.
If I was looking for a second hand truck, I only look for a truck with the regular stock items for that trim level. I don't need any future trouble. Some dealerships mark these improvements down on the trade in as well.
I don't see a $4,000 being ahead - maybe a little but a loss in the trade in because it is still a WT trim level truck.