I know Ford did sell complete engines. Let me check.....
https://performanceparts.ford....part/M-6007-Z2427FRT
They still do. I would initiate a live chat with a Ford tech on there Ford Performance website. When I bought my aluminum Ford block they where very helpful answering a few questions we had. They should be able to tell you what you have and which flywheel and damper you need. Your vibration description does suggest a harmonic caused by something not balanced correctly.
You can cross the transaxle and half-shafts off your list.
Since you purchased a Ford factory crate short block that part should be good to go. I suggest researching and confirming the damper and flywheel are both correct for that application before any dyno work. You need to get that behind you before you get to tuning.