The only holes in the wood are around the edge of the bed, the wheel tubs, and the bed mounting bolts. All the other bolts go through the strips, which are in the gaps between the boards. For the holes on the perimeter, you slide the board in, mark the holes with a Sharpie, remove, drill, bolt in place. You install the wheel tubs last. Boards are in already. Drop on the tub, mark, remove tub, drill (and jigsaw the outline of the inner tub). Bed hold down bolts: mark and drill from the bottom once the bed is in place.
Yes, get wood from an actual lumber place, not a home depot.
This is the first one I did (my truck). Trex, and on big jack stands. More work crawling underneath to do the bolts.
The four side boards in front and back of the tubs go in first. These set the height of the bed, and lock all the cross sills in place. Once you do this, it's simply dropping in the boards, putting on the strips, and bolts bolts bolts.
You can see that side boards are bolted in, strips still to go in here.
Note the gaps between the boards, you can just see the bolt holes in the cross members:
Strips in. Note no strips on the middle two boards so I can remove them, use a strap and my engine hoist to lift the bed on the truck. Once on the truck, bolt down the strips, drill the holes in the boards for the big bolts, done!
Finished product:
If you're building a truck that will be garaged, and the bed won't see rough work, nice stained wood looks great. If your truck will be outside, and working, don't bother with expensive wood/stain. You can see the two very different ones I built, both are nice, both are for different purposes.