Answer #1 (from me): Difficulty making one yourself....on a 10 scale will be a 7-9 depending on which way its built and for what truck, as well as if you want all the bells and whistles(opening struts/locks/ect.). If your a 9 to 5'er and come home and work until dusk, it could possibly be done in about 1 to....well, it depends on your experience, so Ill leave that open.
Answer #2: Yes, its easily possible to get something that large paintably smooth. Again, depending on you.
Answer #3: CrazyOldCougar is good on the 7-12 layers, but even that is dependant on what you use to build the framework. (Ill explain)
Answer #4: Cost depends on your shopping habits. I have on record here with a build we did for a 95 Ranger. The build ONLY for the cover without ANY extras was $197. A local dealer/install shop for the same truck was provided by the owner at the cost of $640+tax. (Ill explain the build)
This "Custom" bed cover was fabricated with a 3 foot wide, and 1inch raised center that started fore and ended aft. The edge of the cover was flush fit to the inside of the bed, which would not be to your waterproof expectancy. The construction consisted of a 1" x 1" angle steel channels welded to build the box edges, also an "X" channel was welded to secure it square. The steel rectangle's measurement was purposely built 1/4 inch shy of touching the edges of each side. A thin sheet of masonite panel lays flat and screwed to the frame. Holes were screwed irratically throughout its surface. Test-fit!!! This is the time to figure its articulation on how its going to move via hinges, struts, locks, ect. After this step, its time to remove it from the truck. Set it up on stands at a low height. Or, it can be hung from the cab end and where the tailgate end it toward the ground. Mix a large amount of resin, apply to the wood, lay FG cloth, roll out the excess resin with roller, immediately apply more resin on top of the FG cloth. This ensures both sides of the FG cloth is soaked in resin, as well as stuck to the wood for secureness. Sand top of each layer. Do this until you have at least completed 5 cured layers. (Explaination: I agreed to CrazyOldCougar because thats how the mass produced bed covers are in thickness on average - some are nearer of 3/4" thick.) BUT, you have an "X" member in the mass of your cover made of steel. Now, lets think.....are you going to put alot of weight on this cover? Why would you put ANYTHING on your nicely painted bedcover?...EVER? Why make this thing weigh more than 3-freaking-hundred lbs? You be the judge. If this thickness is NOT to your liking, resume the operation until satisfied. Next, as a reminder, each time FG cloth is layed, it should also lay over the edge to build up the sides to fill the gap to flush fitting. Finally, finish out the surface with a skin layer of body filler, sand prep for paint.....