Bed alignment seems to be an issue on more than one truck kit that I have built,but I do have one method of correcting it.
What I have done on some of my builds is this..
1)See where the cab and bed mate to the frame.Mark how much space is between the cab and box.If no space,go to step 3.
2)make spacers for the correct gap between the cab and bed,You will use these in step 3 if you do have any gap.
3)align cab and box where you want them,and clamp them together where they will not move.
4)Drill 2 holes with a pin vice bit from the front of the box into the back of the cab(through the spacers if you have them)You will want to place these mount points in an area where they will not be seen,or will be easily filled and sanded flush before paint.
5)run small diameter Evergreen tube through the holes your drilled and glue into position.
Now your cab and box should be perfectly aligned,and should stay that way when you mount to frame.If there is any gap between frame and body mounting points,small spacers can work to get a flush mount,,...