So, lets try to get on the same page. You have referenced main ceiling light, PH upper bed ceiling light, and the rear cargo light.
Are the main "main ceiling light" and "PH upper bed ceiling light" both located on the penthouse ceiling? I assume yes, and both are of the florescent variety.
If yes, these lights both get their 12 volt via the fuse you replaced in the front location.
If not, where is each light located?
All of the rear sporsmobile added lights will come off of the house battery, they should not tied into the Ford Van 12 volt circuits, so don't hunt for ford fuses. There are a couple of things that do tie into the ford front, but they are like the Radio Switch and "Ignition Run" used on some Separators/ACR's.
Fuses are one of the least likely culprits, so the process of just swapping fuses can be pretty fruitless. At some point I will say again you need to invest in a digital multimeter or a test probe such as this
https://www.amazon.com/JASTIND-Backl...s%2C237&sr=8-3
This one happens to have a built in voltage meter, but one with just a light would do. I like this one because it has a relatively long lead wire. You connect the clamp to a good sportsmobile ground , as you touch the probe to a 12 volt source, the probe should light up (or show voltage). generally you can verify the fuse when it is in it's location. The fuse will generally have a probable location on both sides. If they don't pull out the fuse and probe the fuse holder. one side should light up or show voltage.
Yes a wire could be shorted via rubbing via the chassis and shorting out the power, that should have resulted in a blown fuse. If the short is still there then , the new fuse will also blow.
Obviously, the load or in this case lights also have working parts, switch, ballast and bulbs that could go bad. You need to check if the have incoming power again pretty easy with a test probe at the actual unit.
Seeing as two of the lights may be on the same circuit, one would assume that there is some commonality between the failure. Just remember when you assume, so it is better just to check both. You can easily test the switch, with it off one side should light up the test probe, when you turn it on both sides should light up the test probe. If you have power on both sides of the switch, then you are most likely looking at a ballast or bulb issue.
Another often overlooked area is the ground wire, for this circuit to work the ground connection has to go all the way back to the battery. It could be very possible that a wire is broken on more likely a bad connection where they attached the ground wire to the metal body of the van. This is more common than you think with these rigs, they generally are not easy to find. In the case of the Poptop located lights, the ground wire goes up in the same plastic conduit. As you have already seen they appear to use lamp zip cord, for what reason I don't know. One area I would would look would be to track the lamp cord back, one line goes via fuse and other I suspect is screwed into the frame for a ground connection.
I am sure their are videos on using meters and test probes, you are just going to have to invest one, and start probing around. I would practice on circuits you know are working, as it aids in knowing what the result will be. This step should be done whenever you start anyway.
-greg