What is the correct way to measure end play on the input shaft?? If I stand the trans on the tailshaft it's very difficult to get an accurate measurement. With the trans horizontal and the tailshaft pushed back along with the input shaft, when I pull the input shaft forward on the dial I'm reading .045 ??????

I attached the page from my 1973 factory service manual.
IMO, although the two methods you mentioned give slightly different numbers, the main point is to take the measurement both before you take it apart and after you put it back together.

IMO, 0.045" is just fine.

Thanks Jim👍