If there has been a transplant done, are there any warning signs of hackjobs I need to look out for and overall are there any mechanical/operating issues that come from the 6.9L? I am slowly reading up on them but my area of knowledge mainly pertains to the 7.3L motors and the 6.0

 

The 6.9 and 7.3 look very similar from the outside, and the 86-87 6.9 is pretty well identical. The easiest way to tell is the glow plug system, but the later system bolts right on the older engine.
The first Ford pickups with a diesel were actually in Brazil, the F1000 got one in 79. The Courier was sort-of available with the Mazda/Perkins 2200 diesel that was fitted to the 83 Rangers, but I've never heard of one that was actually bought but I have seen a few Mazda B2200s running around.
The C series and N series trucks were available with diesels in the early 60s.