Newb with a 225 needs assistance

The clunk from P to R is a tell-tale sign of bad U-joints (cheap and easy fix). I boiled over my 69 Slant quite a few times, with no problems. Unless you drove a long ways as a Stanley Steamer, I doubt that hurt it. Try basic things first like check tranny fluid, compression, etc.

Before condemning the engine, as a last ditch effort, disconnect the torque converter and push it back and hold it away from the flex plate with a metal strap. See if the engine still makes a noise without the tranny out of the picture. If so, you can get a good 68+ slant tranny for maybe $0 since lots of people go V-8.