I have done Gilbert cars with American Models trucks probably similar to what you want to do. Rusty is right you need to remove the rivet (I just drill), and figure a way to attach the trucks. I have tried various methods. The easiest for me is glue styrene over the hole and drill and tap for a screw.
The other problem is the bolster on Flyer cars is further from the end. The new couplers don't stick out nearly as far. You maybe OK with large large radius curves or use Kadees. The other solution is AM heavy weight passenger couplers. Learned that from Jerry P who posts here. Shimming is needed since the wheels will rub on the frame.
I have no idea if wheel sets can just be replaced. But again not a simple drop in replacement.
