sell the gooseneck and buy one that is compatible with your truck. Or vice versa, You are going to end up with more time and trouble trying to make something work. Your truck has alot of options that make it not so good for the task at hand. You need to get a trailer that is more suitable to your truck.
The hitch offsets are going to farther reduce your safe towing load and make the front end lighter, which will effect handling. And there is not really anything you can do about the bed clearance. Raising the front of the trailer and your going to end up lifting the trailers front axels, doubling the load on the rear axle leading to more problems.
You got a great deal on the trailer, slap on a coat of paint and resell it, find something else.