This is a really interesting source!
However, some of the notes look incorrect (looking at the sources, it's not a big surprise as there's nothing focussed on Livonia). For example, for diocese Revaliensis is noted in 1374 to have become the suffragan of Riga. I have seen this before as well, but only unsourced. In sourced documentation, the Bishop of Reval was documented at the synod of Riga in 1423, but that is the only documentary evidence to consider him a suffragan of Riga. No papal document of this nature survives, and it is far more likely that Reval continued to be a suffragan of Lund until the end of the Middle Ages.
Yeah, I'm not expecting perfect representation, but something approaching "good enough and if someone shows up with a better source I can correct it" representation for 1337. I'm also not planning on following the historical change of who's-suffragan-over-what; I'd rather that be dynamic and be able to adequately reflect the changes that happened historically, rather than mandating that they do happen or rigging up some sort of specific mechanism for specific historical changes.
I would imagine, for instance, that powerful realms would like to try and maintain full control of the ecclesiastical hierarchy that happens to hold sway in their lands (and we see that happen plenty, like Poland demanding the Ecclesiastical Patriarch elevate the Orthodox Bishop of Halych to metropolitan so that it couldn't be placed under control of a Russian archbishop despite the King of Poland being Catholic) and would likely try to force the Pope to organize the Church in their favor. I would see Reval winding up under Riga instead of Lund, for instance, in the event that a state in control of the region managed to have enough control of the region and win enough influence with the Pope to have that reorganization happen in their favor. In that regard, I agree with your assessment.
In the opposite case, I can see the Papacy restructuring bishoprics in areas without a powerful state to better suit their interest, such as breaking it up along cultural lines to facilitate conversion. We see that happen with the Council of Trent, and we
know how that one turned out.
As long as I can get a solid-enough foundation for 1337 and sufficient inspiration for mechanics for transferring suffragan bishops, the circumstances for union/suppression of a diocese, it'll work wonders. Even now it seems like there's a good argument to be made for this mod's existence, because it allows for better representation of the reforms of the Catholic Church being able to happen locally under a sufficiently strong, centralized state even while the rest of the Church fails to deal with widespread corruption (i.e. why the Reformation hit much harder in Germany than it did Spain). Having individual bishops represented lets me model that to an incredible degree.
Honestly I can't wait to start modding this game.
As for sources, right now the ones I need are likely to be Serbia and Bulgaria for Europe. I managed to get access to that book on the Byzantines, so I have a rough outline of what that will look like (it's not exhaustive but at least captures the major bishoprics and the like). Then it's just Georgia, Armenia, and Ethiopia.