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.