Coupla things...
If you have a leak around the lower bowl and the floor, you need to replace that wax ring seal. Never re-use one. When properly installed, you'll have no leak.
Did the floor height rise when your stepdad redid the floor? If so, you'll need to make sure that the throat of the gasket is long enough to accommodate the floor depth. Extensions can be purchased, are are simple to install. Also, make sure that none of the new flooring is obstructing the drain.
If the tank won't refill on it's own, and the water supply is on, then the tank valve is screwed up. Either it's completely out of adjustment, or just plain damaged in the construction. The fill is controlled by a valve located at the top of the tower, where the float and float arm connect. Check that the float moves freely, and is still adjusted correctly.
Frankly, if you're not sure, I'd pull the thing out, reinstall a fresh wax ring and a new replacement tank valve. Replace the supply lines too, if you have those rigid copper ones. Use the flex-braided ones. You're more likely to get a working system the first time, if you're careful.
Good Luck!