What finish can I put on my pallet floor to fill in cracks and have an even, thick top coating?
If you built a floor out of pallet boards I would expect that the floor would be uneven, have cracks between boards and rough surfaces. That style is pretty much what you get with this type of material!!
There is not much that you could do with it except to rip it out and go with something more conventional. You may be able to cover it with a floor leveling material if all the pallet boards are solidly nailed in but then you are still looking at having to install some new floor surface over that.
If this is salvaged wood from pallets, you can sand it all down and groove out all the cracks. Then, you can cut little "Dutchmen" to fit those larger cracks, glue them in, and plane that level with the floor.
If the larger cracks are sealed, you could then coat the floor with a polyurethane or something similar.
Table epoxy comes to mind, but it certainly wouldn't be a cheap solution. Like Michael Karas said, you have to expect a rustic look with pallet wood.