I agree, the cars will sit high with Lionel trucks. However, another option would be to replace the bolster that comes with the kit with a shallower one you fabricate out of wood or styrene.
As for advice, with all wooden kits, if they are models of steel side cars, it helps a lot to treat the wood sides with sanding sealer and sand them a few times before assembly. That way you get them to have a smooth steel look. If it is a model of a wood side car, you can just paint it and let the wood grain show through.
I have used a good wood glue and just was patient to let it set up at each step before moving on. This draws the project out over some time, but gives a sturdy body.
The most important things for operation are to get the holes for the truck mounting centered on the car and to keep the body square during assembly. Every thing else is the "detail" part that adds to looks but not operation.
They are "craftsman" kits, but really work out fine if follow the instructions and work slowly.
On my later caboose kits, I modified the model to have a removable roof so I could glaze the windows after painting.