Only reason I stopped going down the PTA path was I always struggled to figure out a viable way to organize everything.
I tried one file per account, one file per account per month, multiple accounts in one file per month, and eventually everything in one massive file per year. No matter what I seemed to choose I always seemed to end up with just a complete mess.
I've faced this as well. One of the big sources of "mess" for me in a years-long ledger is inconsistencies in account naming. I get around this with a big block of alias that rename accounts to use my newer, preferred conventions (without having to comb through possibly hundreds of postings to update by hand).
I also went through a couple file organization schemes and have (tentatively) settled on file-per-month since that leads to a nice cadence where setting up the new monthly file coincides with paying bills and is a good time to do any necessary account reconciliation.
PTA does give you a lot of flexibility, sometimes too much.
More guidance/opinion on this is probably needed. https://plaintextaccounting.org/Organising-files talks about it a little.
Also if you make it to any of the support fora/chat rooms, you'll usually get help on this.
I tried one file per account, one file per account per month, multiple accounts in one file per month, and eventually everything in one massive file per year. No matter what I seemed to choose I always seemed to end up with just a complete mess.