First - If the "fusible link" on a Samurai fails, the entire vehicle goes dead - on a Samurai, the term "fusible link" refers to a very specific connection, between the battery positive and every circuit in the vehicle except the starter.
Second - you say NO running lights on the right side are working - do you mean neither front nor rear on the right side?
Next - can I assume you have tried a new bulb, or maybe swapped the left & right side bulbs? It's a dual filament bulb and quite possible for one filament to burn out and the other still work.
Assuming it's not as simple as the bulb I need you to conduct a test - have someone hold the brake pedal down (you say the brake lights work) and then watch what happens on the right side when you switch the running lights on - does the brake light still light?
A missing ground can cause all sorts of weird effects - the brake light may be grounding through the running light circuit and appear to work - until you power up the running lights.