To attach the bed sides to the bed floor, I used some pieces of 1/8" x 1" x 1" angle. I used 4 pieces of that angle, one at each front corner, and one at each rear corner. The area between the angles on each side would need to have a gap between the floor and the bed sides filled. Once the position of the bed sides was determined, one leg of the angle was marked and drilled with with (4) 1/4" holes, one hole about 2" from the each end, and the other two holes splitting the distance between the outside holes, those holes were centered on the leg's width. With the holes drilled, the angle was set in place with the holed surface laying on the bed floor, then the other leg of the angles were clamped, leg facing up, to the bed sides at the correct height to position the bed sides at the proper height. All 4 of the bed side angles were stitch welded to the bed sides. After the forward and rearward position of the bed sides on the bed floor was determined, the bed floor was marked through the holes, and the bed sides were pulled out of the way and the holes were drilled to 3/8" diameter through the bed floor. I trimmed near each hole in the bed floor so I could install the 1/4" U-nuts, the 3/8" holes gave me some movement of the U-nuts to make final adjustments to the bed side location before thy were tightened up. I did have to notch the angle near the fuel fill tube to assure clearance, I didn't want to take a chance of the tube rubbing against the angle and cause a possible spark, or a rub through.
Pic 1, This pic shows all 4 angles bolted to the floor and welded into place.
Pic 2, This is the right side bed angles bolted and welded into place. You can also see the gap in the floor between the two pieces of angle, this "cut out" was where the original Dakota wheel well was attached to the bed floor. The Dakota bed was fully welded, I cut the wheel well out of the floor with my plasma cutter, but it could have been cut out with a sawzall with a fine tooth blade. The bed floor in that area is just sheet metal, but reinforcing bracing under the bed is not far away, an under bed inspection before cutting would be a good idea.
Pic 3, This is the right front corner, you can better see the where the wheel well was removed.
Pic 4, This is an overhead shot of the left front corner angle. You can see fuel tube sticking out of the floor and you can see the notch in the angle around the fill tube. The rectangular hole on the left side of the pic is the hole where the battery cables will come up through the floor. That hole is towards the center of the bed, about 1" from that side of the battery. I'm using a pair of "0" size battery cables, the hole is big enough for clearance of both cables, and I made a bracket for the cables to clamp to the floor to prevent damage to them.