The roof markers are not specifically associated with the R05 (dually/wide side) package. They were an available option on fleetside bodies as well. Those 5 roof markers are switched through the same contacts in the H/L switch as the front and rear markers. They connect to the H/L switch at terminal 3 which is normally not used. Terminal 3 is internally jumpered to terminal 5 (the terminal to the T/L & front parking lights):
You must be registered for see images attach
The hot lead to the roof markers is black. It is the only black lead to the H/L switch. You could release it from the harness connector. Then, with markers no longer in the circuit, you could plug the connector back onto the switch and see if the fuse blows. If not, the markers are the problem.
The R05 option includes 9 rear marker lights in addition to the standard two. A front & rear fender clearance lamp (on each side) and the five tail gate markers:
You must be registered for see images attach
Thing is; those extra lights that are required with the R05 set-up are all included in the rear lighting harness. Previously you isolated that group and turned the headlights on. The fuse didn't blow. So, along with the normal markers, tail lights and license plate lighting, you have effectively eliminated all those extra lights.
Since you have done some work in the area behind the cab (the exhaust work, bed removal & gas tank repair), it might be best to ring out the brown lead that goes from the bulkhead connector to the rear harness plug connection.
Release the bolt that secures the plug to the bulkhead connector in the engine compartment. Pull the plug away from the bulkhead connector and locate the terminal for the brown lead to the rear lighting. The female half of the connector (on the firewall) will look something like this:
You must be registered for see images attach
And the male half - that you pulled from the connector - will look kind of like this:
You must be registered for see images attach
Your male plug will look different. It will be made up of 3 sections. One of the sections (the smallest one) will only have 4 wires passing through it. The wires will be colored like this:
You must be registered for see images attach
The block they pass through won't be in that position however. The block for your rear lighting leads will be in the lower right hand corner when looking at the firewall:
You must be registered for see images attach
Locate the brown lead and use your meter to check for continuity to ground. If you get a beep - or a reading of 0 ohms - the short circuit is in the run between the block and the rear harness plug.