I'm sure that yours has been changed to the "7.3 style". The 6.9 controllers could be a HUGE pain. They were known for sticking on and burning out all of your glow plugs. Also, your glow plugs probably have bullet connectors on the tips where the wires hook on. The type that your truck came with had spade connector tips on them. If yours are bullet type, just buy glow plugs for a later model with a 7.3. That will save confusion.
It's possible it was an 87 6.9 engine swap too. My 87 F250 6.9 has the 7.3 style setup and bullet head glow plugs. I know it's stock because if you search for glow plugs for an 87 F250 6.9, you get bullet head ones. Searching for my 85 E350 gets spade ones. Ford switched to the newer system on the 87 6.9, probably since they had changed the assembly line for the upcoming 7.3, just a year early.