I would do the bedliner and cleaning. You can't sell a dirty vehicle, first off. It's an auto, so I wouldn't worry about the e-brake cable, and the leaking manifold isn't that big of a deal. With the muffler, I thought you had pipes coming out the sides? At the most, I would take it to an exhaust shop to put pipes on from the mufflers back, just do it cheap.
Keep in mind, any money you put into the truck would just be to make it sell easier, it's really not going to get you any more money out of it. Someone is going to buy it, probably for what you want out of it, the only difference is how many people look at it and either decide they want it or they don't.