Does anyone have any tips to query all of the transaction lines table to back fill fields? It takes almost a full day to pull just a fraction of the data currently

I'm assuming you are doing this in code by pulling all the data and then using either REST or SOAP to do the backfill? Assuming that's the case then I have always found it effective to run

select min(id) as min_id, max(id) as max_id
from transaction
..... rest of query here

and then create batches of say 100000 ids and add that to the main query. It can make a huge difference to the time to run