Did you look under the rear seats fer the jack? Not sure where they would put the jack handle in the extended cab.
You can search
www.car-part.com fer most of the parts yer looking fer. Mine didn't come with a jack either...ended up buying it from a parts yard 1200 miles away listed in car-part.com...been a deal saver not having to carry a floor jack with me all the time!
As fer the cover...it would depend on the manufacturer and how hard they make it to install. Most are pretty straight forward and easy. I would suggest that you contact the company yer thinking about buying it from and ask them fer the instructions before you make the purchase.
Where the heck is the Berkshires? I've seen a few on craigslist but it would be a bear to ship if you can't git it yerself.