I get that, being a mechanic, I don’t trust garages, I’ve heard too many horror stories tbh, better of figuring it out for yourself.
I think you need to go through a methodical process of elimination, eliminate mechanical possibilities first, then fuel, vacuum, air fuel system, then electrical.
Engine
1. Set up mechanical timing, cam shafts and crank.
2. Check valve clearances (cold engine) and cam chain tension the early busas had a cam chain tensioner mod.
Fuel
1. Check pump pressure from pump to fuel rail, under priming, cranking and revving (once engine is running), pressure should never drop below 42+psi.
2. Injectors
3. Fuel contamination, filters, fuel couloir, smell, water, rust, in tank.
Vacuum.
1. Check for air leaks around vacuum hoses, throttle body boots, electrical connectors to all vacuum sensors
2. Correct vacuum pipe routing from throttle bodies to map sensor.
3. Sync throttle bodies as per workshop manual, after setting TPS.
Electrical
Difficult to suggest a path with electrical but I’d start with water temp switch, map sensor, these affect the fuel/air mix, then I’d start checking voltage, from the stator windings, condition of battery and think about the ckps (crank shaft position sensor), I have first hand experience with a failed one (don’t ask lol).
Coils will usually break down under load, as would plugs but I know busas tend to run rich as standard and this does shorten the life of plugs, maybe worth trying a new set of plugs, it could be something as simple as that?
Hope this helps or if anyone can add something.