I did that conversion on 3 Ford cars over the years. 56 Ford, 69 Mustang and my current 61 Starliner. All 3 had the mounting lugs already in the frame. Covered with grease but they were there.
My 61 Sunliner had the holes but no threads. Had to cut the frame on a scrapped 61 Fairlane to get the weld nuts to put in there. I have done quite a few 50's Ford swaps also and they were always there until this one. 73 Mustang had them too. Maybe they just forgot to put them in this 61..
I just did my 56 but used a T5 transmission. The 5.0 bell housing had no provisions for clutch linkage other than for a cable so I used a cable.