I would make rafts 2'8" x 4' this allows for three rafts per 4x8. I would recommend width of bed to be 51 inches to accommodate 48" raft.
I made my 49 1/2 inches, thinking that 1 1/2 inches would be adequate for lifting raft, but it is a really tight sqeeze and once built you would have to consider cutting down raft for more space.
Just throwing in my 2.4 cents worth.
I recommend at least a few inches of wiggle room at the ends. On long troughs this can easily be achieved by adding 1/4 inch gap between the plywood rips that run down the sides. The 2x4's would have to long enough for the full run. I built 41 foot troughs in the beginning and would go 40' 6" max now. As far as width I now prefer to leave a extra inch(and NO more) of wiggle on the inside for the foam to move. The outside dimension will change depending on the thickness of plywood used. The more room you leave at the ends and sides the more room for algae to grow or in my case more room for duck weed that the birds brought me. I built my troughs at 51 inches inside and had to cover the extra inches of space to prevent extra stuff from growing on uncovered water.
im with Chris on this one, a few inches in the long run is helpful when lifting the boards out. and no more than 1/2" on each side(and you still will see alge) to allow the boards to move. ...im going to say 40' 3"
Dont forget..you are folding liner in the corners, that ads 1/4" to 1/2" to your end wall. i built mine with only an extra 1/2" on sides and ends... its very tight....should have left 1-1/2" to 3 inches on the end to get my hand under the boards.