The choice of basis set for studying conjugated polymers using density functional theory (DFT) calculations can significantly impact the accuracy and computational cost of your calculations. The 6-31G(d,p) basis set is a relatively small and commonly used basis set, but it may not always provide accurate results for conjugated systems due to the potential electron delocalization and long-range electron interactions present in these systems.

For accurate calculations of the electronic properties of conjugated polymers, it is generally recommended to use larger and more sophisticated basis sets that can better describe the electronic structure. Basis sets such as 6-311G(d,p), cc-pVDZ, cc-pVTZ, or even larger basis sets like aug-cc-pVDZ, aug-cc-pVTZ, or their def2 variants (e.g., def2-SVP, def2-TZVP) are often employed for studying conjugated systems. These basis sets include more functions and diffuse functions, which can better capture the electron density distribution in the conjugated systems.

Using a larger basis set will generally improve the accuracy of your results, but it will also increase the computational cost. You mentioned that using the B3LYP functional with the 6-31G(d,p) basis set took about 5 hours. Using a more complex basis set may further increase the computational time required. It is a trade-off between accuracy and computational cost, and you need to consider the balance that suits your specific research goals and available computational resources.

If you have the computational resources and time, it would be worth testing larger basis sets to see if they improve the accuracy of your results for the specific properties you are interested in. Additionally, it is also recommended to benchmark your calculations against experimental data or higher-level theoretical calculations to validate the accuracy of your chosen basis set and functional.