Will a beefed up '78 lil red express express engine tear up a stock 727 torqueflight?

If the trans is in good shape it shouldn't be an issue. Truck LoadFlites got some heavier guts in them just for being a truck transmission. What transfer case do you have? I'd be inclined to be more concerned about that.
Ya good point, it has the NP208. I'll keep an eye out for an NP241, looks like that would be a good alternative