I think you are on the right track. "valve covers, oil pan, rear main, oil cooler" is what I would do.
Leave the heads on. Just get it running. You always have the 6.9 to rebuild if you want.
If you want to do quick and dirty, just swap the 6.9 glow plug system over to the 7.3. The 7.3 GP system is an upgrade. It just depends on your time. Many have added/changed to a manual bypass system with a push button on the dash. I actually prefer mine like this.
The fuel line return system is slightly different too. The 7.3 uses slightly bigger hose on the caps. So I'm thinking you might want to reuse the fuel return system off the 6.9.
The fuel filter system is different too. The 6.9 actually has a finer filter! The stock 7.3 fuel filter has a water blocking element in it with a Water In Fuel detector in the base. The 6.9 has a separate Water Separator located on the drivers side of the firewall.
Many have bypassed this WS and "upgraded" to the 7.3 Filter head as the WS was prone to air intrusion. Mel did a Tech article on cleaning it up.
The piece on the 7.3 pump you were wondering about is called the FIPL or Fuel Injection Pump Lever. It is essentially a Throttle Position Sensor. It is used to determine when the E4OD automatic transmission should shift. You can safely remove it. I think it has two T17 Torx bolts holding it in. Then there is a little collar that comes off. There are two little hex set screws that need to be loosened. Or just leave it on. I would take it off.
BTW, there is a filter on the IP. Its in the cone shaped piece where the fuel enters the pump. To access the filter, you will need to undo the locking tab with a hex key and then un-thread the cone piece from the IP. Use a 3/4" wrench. Have this end pointing up so pieces don't fall out. Pull the cone piece off slowly. Behold, the screen is revealed. If the fuel filter was doing its job, the filter should be clean. The filter just snaps onto the regulator assembly. If you just try and pull the screen up, chances are you will pull the regulator assembly off. That's ok, the regulator assembly has an alignment dowel and the cone piece holds it all in place. Behind the regulator assembly, is the transfer pump. You will see the vanes. Check to see if they are gunked up. If it's all good put it back together! Do this only in
clean dust free environment. Don't touch the vanes with your bare fingers. Use nitril gloves. Tolerances in these IPs is VERY close. It is not in the thousandth of an inch, it is in the millionth of an inch! That is why the fuel filter has a micron rating.
Once you have it all together follow seawalkersee's advice with the starting fluid to bleed it and fire it. Save your glow plugs and battery for when the system is bled. Do not plug in your engine or warm it up prior to using starting fluid.
Use starting fluid/ether only on a cold engine with glow plugs disconnected.