OK, If I understand the problem, your battery is running down and when you disconnect the fuse box, thereby disonnecting ALL the fuses, the battery doesn’t run down. If I’ve got that correct, then one of the many circuits fed by the fuses is likely drawing more current than it should, or is staying on when it shouldn’t. Again, I’m assuming that the vehicle is running fine, and the battery runs down when the engine is off and parked.
The trick to effective trouble-shooting is to: (1)-assume that only ONE thing is wrong, and (2)-start with the EASIEST things first.
A very first check would be to measure the DC voltage across the battery. With a fully charged battery, and with the engine running it should be between 13.8 and 14.7 volts DC. Then shut off the engine and measure the battery voltage again. Without the engine running, it should be around 12.7 volts. If these voltages are OK, you can proceed under the assumption that the charging system and the battery itself are OK.
The next easiest thing to check in your case is to shut off the vehicle and remove the key; then inspect and check to make sure that everything that should be off to make sure that it IS off. Dome light, glove box light, fan, trunk light, under the hood light, cigarette lighter, rear windo defroster, radio, etc.; you get the idea.
If can’t find anything that way, the next easiest thing is to do is to connect a DIGITAL voltmeter across the battery on a low-voltage scale, (above 12 volts) and carefully note the battery voltage. Then remove each fuse, one at a time, and note if there is ANY increase in voltage, even a tiny one. That would mean that something connected to that fuse is drawing current from the battery. From the fuse assignments determine what it is and check to see what is on.
Alternatively, you could connect your DIGITAL meter in series with the battery feed, set to a HIGH ampere setting. Once connected propery, with the proper polarities, reduce the ampere range from highest to lowest until you get a reading on the meter. Again, remove each fuse until the current reading on the meter DROPS, even a tiny bit, and you likely have found a circuit that is continuing to draw current.
Try those things, and if no joy, come back with the results of the tests.
A Haynes manual for your truck will be very helpful in tracing the electrical connections. I recommend you get one if the suggestions above don’t locate the problem.
By the way, you must use a high-impedance meter. One of the newer DIGITAL meters should be adequate. Also, make sure your meter is set to the proper scale and range when using itand pay attention to the polarity connections.
Good luck.