Regarding your mri_vol2vol command, it looks like you’ve been doing some digging in the work directory, which will save you time. The transform from BOLD to T1w space (which is slightly different from FreeSurfer’s T1 space) is bold_reg_wf/bbreg_wf/transformer/transform.mat, not the .dat file.
The above is relevant if you parcellations are volumetric and not surface-based. If they are surface-based, then you’ll either want to do the analysis in the surface or use mri_surf2vol (probably with --fillribbon) to get a volumetric parcellation, which you can use mri_vol2vol to translate.
For a little more context, see Preprocessing for atlas based connectivity matrices.
mri_label2vol will only be useful if you have a .label file, which a cursory glance at the README you linked to suggests not.