How difficult is it

It's not a difficult job if you have the proper tools and knowhow. You also need to have the correct parts so there are no incompatible mismatches. '65 and '69 engines and transmissions are not a direct interchange. The main problem areas are: crankshaft pilot hole for the converters are different diameter, converters for the same reason along with input shaft spline count, engine oil pans (they can and must be swapped over), driveshafts ('69 is slip yoke and '65 is flange type) and cable shift vs. linkage shift on the transmissions along with neutral safety switch/backup light switch, wiring, and function. The transmission as an assy is a '65 only transmission.