The underframe of the kit does not come with pre-defined holes for the coupler box, so you are free to install whichever coupler you want to use. I have standardized on the Walthers HO-scale Proto MAX coupler. The problem with pre-drilled holes is that the two outside tabs on that coupler don't match the typical S-scale Kadee coupler's outside tabs, and so I usually wind up only putting the center screw in the model. This, of course, can lead to the coupler rotating, so I counteract that with some superglue on the back. By not having pre-drilled holes, I can use the two outer tabs to install the screws I want to use for this coupler. To drill the holes exactly where I want them, I put a center mark on both the coupler box lid and the underframe. I stuck some double-sided tape to the coupler box lid, and carefully positioned it where it needs to be. I could then pre-drill the holes, as is shown in the photo.
I then removed the tape and built the coupler, and installed the two screws. I did tap the holes first, as that makes installing the screws go a bit easier. Note that the magnetic-uncoupling hook on the couplers will be cut off at some point as I don't use that method of uncoupling.
The trucks are easier to install. There is a dimple in the underframe for where the hole should be drilled. I drilled that (make sure to keep the drill as perpendicular to the underframe as possible), and used a tap to put the spiral grooves in the hole. There is a lot of material to drill through here, which is a good thing, but it will take a bit of time to do so. I am using a pair of MTH trucks I have left over, which are not the correct style of trucks to use, but they will have to do until I can get a pair that is correct. Wiseman Model Services has a kit of the correct type of truck, but this car's kit instructions state the Pre-Size may produce their own.