Your description of the problem smells a bit like job-shop scheduling. Optimizing job-shop scheduling is NP-Hard, so at best one general purpose algorithm might be better than another, but you can't determine which by simple inspection. Efficiency will vary based on the actual details of your data.
The standard approach (after managing IO) is to tune for the regularities in your data. Regularities are what makes your arbitrary data arbitrary data and not random values. Tuning the algorithm can get you a long way in the time domain. No data structure alone can get you out of NP. Good luck.
Your description of the problem smells a bit like job-shop scheduling. Optimizing job-shop scheduling is NP-Hard, so at best one general purpose algorithm might be better than another, but you can't determine which by simple inspection. Efficiency will vary based on the actual details of your data.
The standard approach (after managing IO) is to tune for the regularities in your data. Regularities are what makes your arbitrary data arbitrary data and not random values. Tuning the algorithm can get you a long way in the time domain. No data structure alone can get you out of NP. Good luck.