Glad to hear that the engine swap is nearly complete. Take it easy and checkthe oli often as well as keep an eye on the oil pressure.
As to the damage. The tow company should have to pay for the repairs. The lower front and rear wraps are made of ABS. And as far as I know are NLA (No Longer Available). They can be repaired with fiberglass and paint. Unless you signed a damage wavier they are liable for any damage they cause on your vehicle.
You may want to have it estimated and at the least get a check. It can help offset the Enormous repair costs that you have incurred.
I would not let them ( a bodyshop) drive my brand new motor.