You'll want to pull the injectors and have a buddy crank the engine and watch the spray pattern. If they stream or sputter, that can be the issue, each one should put out a nice mist spray. If the spray patterns look okay, you could test each injector to make sure it pops at the proper psi as specified in the tech manual, I don't remember the exact psi, but there are plenty of threads on here where it's discussed and others sharing their methods to test the injector. If an injector has a poor spray pattern, it could be dirty and just needs to be disassembled and cleaned or could be worn and needs rebuilt or replaced. Being a mechanical engine, I find it unlikely any power source can cause a misfire. Only other possibility is that the misfire was misdiagnosed as a surge due to dirty fuel filters, which I can see that being a possibility as surges can sometimes feel like a misfire, but being you changed the filters amd really black smoke is a big indicator of unburnt fuel, I believe it to an injector issue.