It may be conditioning at this point. it will be hard to tell if you have fixed the problem right away unless you can have someone in the back coaching and giving active support. another way to try at this could be to get in the truck with the dog once a day, ignition full off. just hang out and be cool with the dog, give treats, do something the dog likes to get over the digging in anxiety against entering the truck.
then keep up the same routine on the truck (after installing that strip for bed to cab) and start the truck. don't go anywhere, just hang out and be cool.
Move on to low speed neighborhood driving if you get the dog comfortable with running idle. avoid more than 25-30mph to keep any seal noises to the least possible wind loading.
If that works out, move up to in town driving with all windows ajar enough to prevent the buffeting and keep air circulating. most dogs love the smells and travel fresh air.
My point is basically try to break down the problem and the retraining into as small of bits as you can. know that even if you have fixed the problem you will still have work to do.
If this doesn't work out, I'm the kind of guy who would buy a second, limited use vehicle for the dog needs because my dog is my family. if you can bear the expense, a trade out may be what is called for. you would be surprised what the difference a new color or smell of a truck will do to break the anxiety and possibly even fix the root issue that you were having (though then you get into the whole pile of new vehicle issues unrelated).
Seriously, good luck. I'm hoping that you get this sorted for your pet and family's comfort and happiness.
