If I'm reading you right, you've got the transmission bolted to your crossmember at the rear, and the engine bolted in on the side motor mounts. I don't know about your truck specifically, but most vehicles only have those three points of contact. You should be fine with that.
As far as your crossmember goes: if it's a 3" box channel, it should definately be strong enough, and if it fits and keeps everything lined up properly, you're golden.
