I've had an issue like this with some 3D printed body shells I've had made. I have the trucks you picture although I did not use them for this project and yes, they came without mounting screws.
I think that with these trucks there's a single washerhead screw that mounts each truck to the the stamped metal frame or the underside of the freight car body. The truck screw is fixed into the top center of the truck through the frame or body shell; you will have seen the threaded screw hole in the top of each truck. I would have thought that the screw holes you need to provide in your 3D printed model should be no larger diameter than that hole but there is a little bit more to the mounting than that.
Most stamped metal frames that I have seen have a sort of small dome where the truck screw is located that is pointed down towards that truck mounting hole, which I assume is to ensure that the truck can turn freely without binding on the frame. I suppose that you could have something like that moulded into your 3D printing or use plastic washers to create the same effect.
The screw size and thread that is used varies with the specific type of truck. You can test fit a few at any hardware store like Ace that has a machine screw section. I think that these trucks may use something like the part shown below, which is a metric washerhead screw 3 mm in diameter with a .5" thread although some Lionel truck mounting screws are in imperial measurements; it's a matter of test fitting a few standard screws to see what fits.