To use that egine/tranny combo, you're going to have to use some sort of aftermarket mounting system. For the engine, you'll need to use the type that uses the side mounts, like the aftermarket crossmember in Seons post. There are also side mounts that bolt to the frame that do not have the crossmember, available from Speedway and JCW. For the trans, you'll need a tranny mount crossmember, similar to the engin crossmembe, only with a transmission mounting pad. The original rear sidemounts won't work with the later trans, and it needs support at the rear.
I'd suggest the you look into the bolt in style mounts as to keep damage to the powdercoat to a minimum. Check with Speedway, Jegs, or Summit. All three carry universal mounts just for this type of conversion.