With a little insight and inspiration from member 07_F150_XLT_Scab I modified a tonneau cover to fit my bed.
The area to be covered was about 4'-6" due to a toolbox and ladder rack.

I won a Ford factory cover of Ebay for $29.99 with "local pickup". Pick up was about an hour each way so with gas and tolls I got about $55 in this cover.

I took some measurements then started cutting. Overlapped the front section and sewed with 10lb Firewire fishing line. Broke 4 needles. To get through the plastic I used a small drill bit so the needle would get through it.

Had to raise the tool box so I could access the latches. Between the tool box and the front rail I put in a piece of wood then wrapped it with some leftover piece of the cover.

Now I can keep a lot of my tools in the bed instead of the cab when its raining or snowing.

 

Nice job, looks great!

 

Im going to be buying a box for my truck in the next couple weeks. I will need to make my cover shorter but im nervous about ruining it. Paid $300 for it. Do you have any more pics of the all the steps?

 

BennyBoi, if you don't want to have to cut your current cover, we make a roll-up cover that's meant to be installed with most 19"-21" over-the-rails toolboxes: http://www.agricover.com/access/toolbox/

You could sell your old cover and have a new cover with a warranty that will last as long as you own your truck. If I can help you with anything, please let me know.

 

If I didnt have the removable ladder racks thus having a gap between the tool box and the front bed rail I'd would have gone the Access cover route.

BennyBoi, I dont have any more pics. What I did was cut the side rails to length and mounted the rails to my bed. Then measured the overall length. On my cover and I guess on all covers the cover slides into the front channel so I measured from the front off the cover and cut about 4".
I laid the cover upside down on the floor and measured the length I needed and then put the cut front piece over the cover. I taped everything down and remeasured the length. I sewed the front piece to the cover. Then I turned the cover over like it goes on the truck and then drilled through the plastic and sewed the cover to the front cover section.
You can see my wonderful sewing job in the first pic. If you do decide to cut your cover I can take a pic of the underside of the cover where I stitched everything together.

 

Looks good..... Thumbs up! Yours turned out just as good as mine if not better. I hadn't thought about lifting my box up, but I just use it for my jack and straps