Top brake light is not working

OK I'm jumping in the middle but if I've read this correctly, you started out with the rear brake lights working but not the one CHMSL on the top of the cab? You traced some wires and found the illumination fuse 14 feed was smoking? Now you have most of it working?

The inner two bulbs on the CHMSL light are the brake bulbs, they are fed on a white wire from the brake light switch. The two outer lamps are the box lights. They are fed with an almost identical white wire BUT get their feed from the cargo switch through the same feed that powers the interior lights.
Easy way to determine which is to step on the brakes with the cargo switch off and use a test light, the white wire with power is the brake feed.

The only gray wire I see goes from the interior light switch to the interior light control module.

Below are the three diagrams for the interior and CHSML lights (left) and the turn/marker/brake lamps as they all interconnect.

The brake/turn light should only flash with the hazard or turn lights. It sounds like you have a bad ground feeding back if the CHMSL is flashing.

Hope that helps some.

OK does the cargo light come on with the dome light if you have the cargo switch on?
If that works but still doesn't shut off you will want to check the interior lighting module. The door switches tell it to turn those lights on/off. Check to see if the switch is actually working. Have seen them fail a bunch.

It is in the middle of the dash tucked up underneath. BUT only if you don't have remote keyless entry. If you have that the module is part of the RKE module not a stand alone. Look for 5 wire connector with wire colors: gray, white, orange, pink & black.

Don't have which? Remote or no lighting control module?

What purple? The only purple wire I find is for the switch that allows you to turn on/off the dome and cargo lights with the dimmer at the headlight switch. If you connect to that wire you bypass the switch and won't be able to turn the dome lights on off with that switch.

Easiest way is using a test light connected to battery positive. With it the light comes on when the tip touches a ground.

Which lights do you want to test. The interior lights get power full time on one side of the socket on the orange wire. Connect the test light to ground, then test the light socket. One side should light the light. The other side (white) is the grounded side.
The lights are ground switched. IE: the door switches and panel switch supply a ground to the lights through the lighting control. Test the ground on that first. Test light connected to battery power will light up if it's grounded at the black wire.

There won't be power to the door switches they are on the ground side of the system.
They ground out and tell the lighting module to turn on the lights. If they are working you should be able to connect a test light to power and touch the other end to the purple wire at each switch and it should light. It should also light at the gray wire on the dome defeat switch in one switch position. With that switch on the light should light at every other gray wire as well.

If you look at the schematic you can see there is a purple wire that is loose and tagged an not used.

You should have power at the pink wire with the key on and at the orange wire full time on the module. If the door switches are working and a door is open you should also see power on the white wire. Black wire goes to ground. If you connect the gray wire to ground the white wire should power on, that is what the switches do.