Trying to lower that engine and trans together will be a swear fest and ultimately to no avail. You can’t get the tail of the tranny over the crossmember without have the nose of the engine foul on the rad support. All made doubly difficult without a load shifter to tilt the engine.
I think you’re better off to separate engine and tranny again, and while it’s apart, check the pilot bushing against that input shaft. You should NOT need to pull that trans in with the bolts. If that’s how you did it, it may be a bitch to separate them again. 🤬